From 1e64ab3dd676ba40af91e7924a8d1737e9e3e87c Mon Sep 17 00:00:00 2001 From: =?utf8?q?Carn=C3=AB=20Draug?= Date: Fri, 8 Sep 2017 21:23:06 +0100 Subject: [PATCH] Removal of Bio::Tools::Phylo::PAML.pm and related modules, tests, and docs --- Bio/Tools/Phylo/PAML.pm | 1872 ---------------------------- Bio/Tools/Phylo/PAML/Codeml.pm | 255 ---- Bio/Tools/Phylo/PAML/ModelResult.pm | 564 --------- Bio/Tools/Phylo/PAML/Result.pm | 1238 ------------------ scripts/utilities/bp_pairwise_kaks.pl | 211 ---- t/Tools/Phylo/PAML.t | 545 -------- t/data/M0.mlc | 159 --- t/data/aaml.mlc | 54 - t/data/aaml_pairwise.mlc | 49 - t/data/baseml.pairwise | 31 - t/data/baseml.usertree | 42 - t/data/branchSite.mlc | 115 -- t/data/bug3331.mlc | 128 -- t/data/codeml.mlc | 190 --- t/data/codeml315.mlc | 132 -- t/data/codeml4.mlc | 230 ---- t/data/codeml43.mlc | 231 ---- t/data/codeml43_nssites.mlc | 251 ---- t/data/codeml45.mlc | 460 ------- t/data/codeml_lysozyme/2NG.dN | 8 - t/data/codeml_lysozyme/2NG.dS | 8 - t/data/codeml_lysozyme/2NG.tt | 8 - t/data/codeml_lysozyme/4fold.nuc | 26 - t/data/codeml_lysozyme/lnf | 170 --- t/data/codeml_lysozyme/lysozymeSmall.ctl | 37 - t/data/codeml_lysozyme/lysozymeSmall.trees | 36 - t/data/codeml_lysozyme/lysozymeSmall.txt | 64 - t/data/codeml_lysozyme/mlc | 273 ---- t/data/codeml_lysozyme/rst | 1165 ----------------- t/data/codeml_lysozyme/rst1 | 1 - t/data/codeml_lysozyme/rub | 48 - t/data/codeml_nan.mlc | 177 --- t/data/codeml_nssites.mlc | 329 ----- t/data/singleNSsite.mlc | 152 --- t/data/yn00.mlc | 106 -- t/data/yn00_45.mlc | 595 --------- 36 files changed, 9960 deletions(-) delete mode 100644 Bio/Tools/Phylo/PAML.pm delete mode 100644 Bio/Tools/Phylo/PAML/Codeml.pm delete mode 100644 Bio/Tools/Phylo/PAML/ModelResult.pm delete mode 100644 Bio/Tools/Phylo/PAML/Result.pm delete mode 100644 scripts/utilities/bp_pairwise_kaks.pl delete mode 100644 t/Tools/Phylo/PAML.t delete mode 100644 t/data/M0.mlc delete mode 100644 t/data/aaml.mlc delete mode 100644 t/data/aaml_pairwise.mlc delete mode 100644 t/data/baseml.pairwise delete mode 100644 t/data/baseml.usertree delete mode 100644 t/data/branchSite.mlc delete mode 100644 t/data/bug3331.mlc delete mode 100644 t/data/codeml.mlc delete mode 100644 t/data/codeml315.mlc delete mode 100644 t/data/codeml4.mlc delete mode 100644 t/data/codeml43.mlc delete mode 100644 t/data/codeml43_nssites.mlc delete mode 100644 t/data/codeml45.mlc delete mode 100644 t/data/codeml_lysozyme/2NG.dN delete mode 100644 t/data/codeml_lysozyme/2NG.dS delete mode 100644 t/data/codeml_lysozyme/2NG.tt delete mode 100644 t/data/codeml_lysozyme/4fold.nuc delete mode 100644 t/data/codeml_lysozyme/lnf delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.ctl delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.trees delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.txt delete mode 100644 t/data/codeml_lysozyme/mlc delete mode 100644 t/data/codeml_lysozyme/rst delete mode 100644 t/data/codeml_lysozyme/rst1 delete mode 100644 t/data/codeml_lysozyme/rub delete mode 100644 t/data/codeml_nan.mlc delete mode 100644 t/data/codeml_nssites.mlc delete mode 100644 t/data/singleNSsite.mlc delete mode 100644 t/data/yn00.mlc delete mode 100644 t/data/yn00_45.mlc diff --git a/Bio/Tools/Phylo/PAML.pm b/Bio/Tools/Phylo/PAML.pm deleted file mode 100644 index 32d7f6bbb..000000000 --- a/Bio/Tools/Phylo/PAML.pm +++ /dev/null @@ -1,1872 +0,0 @@ -# -# BioPerl module for Bio::Tools::Phylo::PAML -# -# Please direct questions and support issues to -# -# Cared for by Jason Stajich -# -# Copyright Jason Stajich, Aaron J Mackey -# -# You may distribute this module under the same terms as perl itself - -# POD documentation - main docs before the code - -=head1 NAME - -Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, -baseml, basemlg, codemlsites and yn00 - -=head1 SYNOPSIS - - #!/usr/bin/perl -Tw - use strict; - - use Bio::Tools::Phylo::PAML; - - # need to specify the output file name (or a fh) (defaults to - # -file => "codeml.mlc"); also, optionally, the directory in which - # the other result files (rst, 2ML.dS, etc) may be found (defaults - # to "./") - my $parser = Bio::Tools::Phylo::PAML->new - (-file => "./results/mlc", -dir => "./results/"); - - # get the first/next result; a Bio::Tools::Phylo::PAML::Result object, - # which isa Bio::SeqAnalysisResultI object. - my $result = $parser->next_result(); - - # get the sequences used in the analysis; returns Bio::PrimarySeq - # objects (OTU = Operational Taxonomic Unit). - my @otus = $result->get_seqs(); - - # codon summary: codon usage of each sequence [ arrayref of { - # hashref of counts for each codon } for each sequence and the - # overall sum ], and positional nucleotide distribution [ arrayref - # of { hashref of frequencies for each nucleotide } for each - # sequence and overall frequencies ]: - my ($codonusage, $ntdist) = $result->get_codon_summary(); - - # example manipulations of $codonusage and $ntdist: - printf "There were %d %s codons in the first seq (%s)\n", - $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id(); - printf "There were %d %s codons used in all the sequences\n", - $codonusage->[$#{$codonusage}]->{AAA}, 'AAA'; - printf "Nucleotide %c was present %g of the time in seq %s\n", - 'A', $ntdist->[1]->{A}, $otus[1]->id(); - - # get Nei & Gojobori dN/dS matrix: - my $NGmatrix = $result->get_NGmatrix(); - - # get ML-estimated dN/dS matrix, if calculated; this corresponds to - # the runmode = -2, pairwise comparison usage of codeml - my $MLmatrix = $result->get_MLmatrix(); - - # These matrices are length(@otu) x length(@otu) "strict lower - # triangle" 2D-matrices, which means that the diagonal and - # everything above it is undefined. Each of the defined cells is a - # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", - # "S" and "N". If a ML matrix, "lnL" and "kappa" will also be defined. - printf "The omega ratio for sequences %s vs %s was: %g\n", - $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega}; - - # with a little work, these matrices could also be passed to - # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building - # method that accepts a matrix of "distances" (using the LOWTRI - # option): - my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ]; - - # for runmode's other than -2, get tree topology with estimated - # branch lengths; returns a Bio::Tree::TreeI-based tree object with - # added PAML parameters at each node - my ($tree) = $result->get_trees(); - for my $node ($tree->get_nodes()) { - # inspect the tree: the "t" (time) parameter is available via - # $node->branch_length(); all other branch-specific parameters - # ("omega", "dN", etc.) are available via - # ($omega) = $node->get_tag_values('omega'); - } - - # if you are using model based Codeml then trees are stored in each - # modelresult object - for my $modelresult ( $result->get_NSSite_results ) { - # model M0, M1, etc - print "model is ", $modelresult->model_num, "\n"; - my ($tree) = $modelresult->get_trees(); - for my $node ($tree->get_nodes()) { - # inspect the tree: the "t" (time) parameter is available via - # $node->branch_length(); all other branch-specific parameters - # ("omega", "dN", etc.) are available via - # ($omega) = $node->get_tag_values('omega'); - } - } - - # get any general model parameters: kappa (the - # transition/transversion ratio), NSsites model parameters ("p0", - # "p1", "w0", "w1", etc.), etc. - my $params = $result->get_model_params(); - printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1}; - - # parse AAML result files - my $aamat = $result->get_AADistMatrix(); - my $aaMLmat = $result->get_AAMLDistMatrix(); - -=head1 DESCRIPTION - -This module is used to parse the output from the PAML programs codeml, -baseml, basemlg, codemlsites and yn00. You can use the -Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the -PAML programs, but this module is only useful to parse the output. - -This module has fledgling support for PAML version 4.3a (October 2009). -Please report any problems to the mailing list (see FEEDBACK below). - -=head1 TO DO - -Implement get_posteriors(). For NSsites models, obtain arrayrefs of -posterior probabilities for membership in each class for every -position; probabilities correspond to classes w0, w1, ... etc. - - my @probs = $result->get_posteriors(); - - # find, say, positively selected sites! - if ($params->{w2} > 1) { - for (my $i = 0; $i < @probs ; $i++) { - if ($probs[$i]->[2] > 0.5) { - # assumes model M1: three w's, w0, w1 and w2 (positive selection) - printf "position %d: (%g prob, %g omega, %g mean w)\n", - $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3]; - } - } - } else { print "No positive selection found!\n"; } - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to -the Bioperl mailing list. Your participation is much appreciated. - - bioperl-l@bioperl.org - General discussion - http://bioperl.org/wiki/Mailing_lists - About the mailing lists - -=head2 Support - -Please direct usage questions or support issues to the mailing list: - -I - -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem -with code and data examples if at all possible. - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via the -web: - - https://github.com/bioperl/bioperl-live/issues - -=head1 AUTHOR - Jason Stajich, Aaron Mackey - -Email jason-at-bioperl.org -Email amackey-at-virginia.edu - -=head1 CONTRIBUTORS - -Albert Vilella avilella-AT-gmail-DOT-com -Sendu Bala bix@sendu.me.uk -Dave Messina dmessina@cpan.org - -=head1 TODO - -RST parsing -- done, Avilella contributions bug#1506, added by jason 1.29 - -- still need to parse in joint probability and non-syn changes - at site table - -=head1 APPENDIX - -The rest of the documentation details each of the object methods. -Internal methods are usually preceded with a _ - -=cut - -# Let the code begin... - -package Bio::Tools::Phylo::PAML; -use vars qw($RSTFILENAME); -use strict; - -# Object preamble - inherits from Bio::Root::Root - -use base qw(Bio::Root::Root Bio::Root::IO Bio::AnalysisParserI); - -BEGIN { - $RSTFILENAME = 'rst'; # where to get the RST data from -} - -# other objects used: -use IO::String; -use File::Spec; -use Bio::TreeIO; -use Bio::Tools::Phylo::PAML::Result; -use Bio::LocatableSeq; -use Bio::PrimarySeq; -use Bio::Matrix::PhylipDist; -use Bio::Tools::Phylo::PAML::ModelResult; - -=head2 new - - Title : new - Usage : my $obj = Bio::Tools::Phylo::PAML->new(%args); - Function: Builds a new Bio::Tools::Phylo::PAML object - Returns : Bio::Tools::Phylo::PAML - Args : Hash of options: -file, -fh, -dir - -file (or -fh) should contain the contents of the PAML - outfile; - -dir is the (optional) name of the directory in - which the PAML program was run (and includes other - PAML-generated files from which we can try to gather data) - -=cut - -sub new { - - my ( $class, @args ) = @_; - - my $self = $class->SUPER::new(@args); - $self->_initialize_io(@args); - my ($dir) = $self->_rearrange( [qw(DIR)], @args ); - $self->{_dir} = $dir if defined $dir; - return $self; -} - -=head2 Implement Bio::AnalysisParserI interface - -=cut - -=head2 next_result - - Title : next_result - Usage : $result = $obj->next_result(); - Function: Returns the next result available from the input, or - undef if there are no more results. - Example : - Returns : a Bio::Tools::Phylo::PAML::Result object - Args : none - -=cut - -sub next_result { - - my ($self) = @_; - my %data; - - # parse the RST file, if it doesn't exist or if dir is not set - # this will just skip the parsing - $self->_parse_rst(); - my $idlookup; # a hashreference to SEQID (number) ==> 'SEQUENCENAME' - # get the various codon and other sequence summary data, if necessary: - $self->_parse_summary - unless ( $self->{'_summary'} && !$self->{'_summary'}->{'multidata'} ); - - # OK, depending on seqtype and runmode now, one of a few things can happen: - my $seqtype = $self->{'_summary'}->{'seqtype'}; - if ( $seqtype eq 'CODONML' || $seqtype eq 'AAML' ) { - my $has_model_line = 0; - while ( defined( $_ = $self->_readline ) ) { - if ( $seqtype eq 'CODONML' - && m/^pairwise comparison, codon frequencies:/ ) - { - - # runmode = -2, CODONML - $self->debug("pairwise Ka/Ks\n"); - $self->_pushback($_); - %data = $self->_parse_PairwiseCodon; - last; - } - elsif ( $seqtype eq 'AAML' && m/^ML distances of aa seqs\.$/ ) { - $self->_pushback($_); - - # get AA distances - %data = ( '-AAMLdistmat' => $self->_parse_aa_dists() ); - - # $self->_pushback($_); - # %data = $self->_parse_PairwiseAA; - # last; - } - elsif ( - m/^Model\s+(\d+)/ - || ( ( !$has_model_line && m/^TREE/ ) - && $seqtype eq 'CODONML' - && ($self->{'_summary'}->{'version'} !~ /4/)) - # last bit to keep PAML >= 4 from being caught here - # bug 2482. Not sure this is the right fix, but tests - # pass and the bug's test case passes. - ) - { - $self->_pushback($_); - my $model = $self->_parse_NSsitesBatch; - push @{ $data{'-NSsitesresults'} }, $model; - $has_model_line = 1; - } - elsif (m/for each branch/) { - my %branch_dnds = $self->_parse_branch_dnds; - if ( !defined $data{'-trees'} ) { - $self->warn( - "No trees have been loaded, can't do anything\n"); - next; - } - my ($tree) = @{ $data{'-trees'} }; - if ( !$tree - || !ref($tree) - || !$tree->isa('Bio::Tree::Tree') ) - { - $self->warn("no tree object already stored!\n"); - next; - } - - # These need to be added to the Node/branches - while ( my ( $k, $v ) = each %branch_dnds ) { - - # we can probably do better by caching at some point - my @nodes; - for my $id ( split( /\.\./, $k ) ) { - my @nodes_L = - map { $tree->find_node( -id => $_ ) } - @{ $idlookup->{$id} }; - my $n = - @nodes_L < 2 - ? shift(@nodes_L) - : $tree->get_lca(@nodes_L); - if ( !$n ) { - $self->warn("no node for $n\n"); - } - unless ( $n->is_Leaf && $n->id ) { - $n->id($id); - } - push @nodes, $n; - } - my ( $parent, $child ) = @nodes; - while ( my ( $kk, $vv ) = each %$v ) { - $child->add_tag_value( $kk, $vv ); - } - } - } - elsif (m/^TREE/) { - - # runmode = 0 - $self->_pushback($_); - ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; - - #last; - } - elsif (m/Heuristic tree search by stepwise addition$/) { - - # runmode = 3 - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => "StepwiseAddition not yet implemented!" - ); - - # $self->_pushback($_); - # %data = $self->_parse_StepwiseAddition; - # last; - - } - elsif (m/Heuristic tree search by NNI perturbation$/) { - - # runmode = 4 - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => "NNI Perturbation not yet implemented!" - ); - - # $self->_pushback($_); - # %data = $self->_parse_Perturbation; - # last; - - } - elsif (m/^stage 0:/) { - - # runmode = (1 or 2) - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => "StarDecomposition not yet implemented!" - ); - - $self->_pushback($_); - %data = $self->_parse_StarDecomposition; - last; - } - } - } - elsif ( $seqtype eq 'BASEML' ) { - while ( defined( $_ = $self->_readline ) ) { - if (/^Distances:/) { - $self->_pushback($_); - my ( $kappa, $alpha ) = $self->_parse_nt_dists(); - %data = ( - '-kappa_distmat' => $kappa, - '-alpha_distmat' => $alpha - ); - } - elsif (/^TREE/) { - $self->_pushback($_); - ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; - } - } - } - elsif ( $seqtype eq 'YN00' ) { - while ( $_ = $self->_readline ) { - if ( -m/^Estimation by the method|\(B\) Yang & Nielsen \(2000\) method/ - ) - { - $self->_pushback($_); - %data = $self->_parse_YN_Pairwise; - last; - } - } - } - if (%data) { - $data{'-version'} = $self->{'_summary'}->{'version'}; - $data{'-seqs'} = $self->{'_summary'}->{'seqs'}; - $data{'-patterns'} = $self->{'_summary'}->{'patterns'}; - $data{'-ngmatrix'} = $self->{'_summary'}->{'ngmatrix'}; - $data{'-codonpos'} = $self->{'_summary'}->{'codonposition'}; - $data{'-codonfreq'} = $self->{'_summary'}->{'codonfreqs'}; - $data{'-model'} = $self->{'_summary'}->{'model'}; - $data{'-seqfile'} = $self->{'_summary'}->{'seqfile'}; - $data{'-aadistmat'} = $self->{'_summary'}->{'aadistmat'}; - $data{'-stats'} = $self->{'_summary'}->{'stats'}; - $data{'-aafreq'} = $self->{'_summary'}->{'aafreqs'}; - $data{'-ntfreq'} = $self->{'_summary'}->{'ntfreqs'}; - $data{'-input_params'} = $self->{'_summary'}->{'inputparams'}; - $data{'-rst'} = $self->{'_rst'}->{'rctrted_seqs'}; - $data{'-rst_persite'} = $self->{'_rst'}->{'persite'}; - $data{'-rst_trees'} = $self->{'_rst'}->{'trees'}; - return Bio::Tools::Phylo::PAML::Result->new(%data); - } - else { - return; - } -} - -sub _parse_summary { - my ($self) = @_; - - # Depending on whether verbose > 0 or not, and whether the result - # set comes from a multi-data run, the first few lines could be - # various things; we're going to throw away any sequence data - # here, since we'll get it later anyways - - # multidata ? : \n\nData set 1\n - # verbose ? : cleandata ? : \nBefore deleting alignment gaps. \d sites\n - # [ sequence printout ] - # \nAfter deleting gaps. \d sites\n" - # : [ sequence printout ] - # CODONML (in paml 3.12 February 2002) <<-- what we want to see! - - my $SEQTYPES = qr( (?: (?: CODON | AA | BASE | CODON2AA ) ML ) | YN00 )x; - my $line; - $self->{'_already_parsed_seqs'} = $self->{'_already_parsed_seqs'} ? 1 : 0; - my @lines; - while ( $_ = $self->_readline ) { - push @lines, $_; - if (m/^($SEQTYPES) \s+ # seqtype: CODONML, AAML, BASEML, CODON2AAML, YN00, etc - (?: \(in \s+ ([^\)]+?) \s* \) \s* )? # version: "paml 3.12 February 2002"; not present < 3.1 or YN00 - (\S+) \s* # tree filename - (?: (.+?) )? # model description (not there in YN00) - \s* $ # trim any trailing space - /ox - ) - { - @{ $self->{'_summary'} }{qw(seqtype version seqfile model)} = - ( $1, $2, $3, $4 ); - - # in 4.3, the model is on its own line - if ( !defined $self->{'_summary'}->{'model'} ) { - my $model_line = $self->_readline; - chomp $model_line; - if ($model_line =~ /^Model:/) { - $self->{'_summary'}->{'model'} = $model_line; - } - } - - defined $self->{'_summary'}->{'model'} - && $self->{'_summary'}->{'model'} =~ s/Model:\s+//; - $self->_pushback($_) - if $self->{'_summary'}->{'seqtype'} eq 'AAMODEL'; - last; - } - elsif ((m/\s+?\d+?\s+?\d+?/) && ( $self->{'_already_parsed_seqs'} != 1 )) { - $self->_parse_seqs; - } - elsif (m/^Data set \d$/) { - $self->{'_summary'} = {}; - $self->{'_summary'}->{'multidata'}++; - } - elsif (m/^Before\s+deleting\s+alignment\s+gaps/) { #Gap - my ($phylip_header) = $self->_readline; - $self->_parse_seqs; - } - elsif ( ( @lines >= 3 ) && ( $self->{'_already_parsed_seqs'} != 1 ) ) - { #No gap - # don't start parsing seqs yet if we're on a blank line - # (gives another opportunity to match one of the other regexes) - unless (/^\n$/) { - $self->_parse_seqs; - } - } - elsif ( (/Printing out site pattern counts/) - && ( $self->{'_already_parsed_seqs'} != 1 ) ) { - $self->_parse_patterns; - } - } - - unless ( defined $self->{'_summary'}->{'seqtype'} ) { - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => 'Unknown format of PAML output did not see seqtype' - ); - } - my $seqtype = $self->{'_summary'}->{'seqtype'}; - if ( $seqtype eq "CODONML" ) { - $self->_parse_inputparams(); # settings from the .ctl file - # that get printed - $self->_parse_patterns(); # codon patterns - not very interesting - $self->_parse_seqs(); # the sequences data used for analysis - $self->_parse_codoncts(); # counts and distributions of codon/nt - # usage - $self->_parse_codon_freqs(); # codon frequencies - $self->_parse_distmat(); # NG distance matrices - } - elsif ( $seqtype eq "AAML" ) { - $self->_parse_inputparams; - $self->_parse_patterns(); - $self->_parse_seqs(); # the sequences data used for analysis - $self->_parse_aa_freqs(); # AA frequencies - # get AA distances - $self->{'_summary'}->{'aadistmat'} = $self->_parse_aa_dists(); - - } - elsif ( $seqtype eq "CODON2AAML" ) { - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => 'CODON2AAML parsing not yet implemented!' - ); - } - elsif ( $seqtype eq "BASEML" ) { - $self->_parse_patterns(); - $self->_parse_seqs(); - $self->_parse_nt_freqs(); - - } - elsif ( $seqtype eq "YN00" ) { - $self->_parse_codon_freqs(); - $self->_parse_codoncts(); - $self->_parse_distmat(); # NG distance matrices - } - else { - $self->throw( - -class => 'Bio::Root::NotImplemented', - -text => 'Unknown seqtype, not yet implemented!', - -value => $seqtype - ); - } - -} - -sub _parse_inputparams { - my ($self) = @_; - while ( defined( $_ = $self->_readline ) ) { - if (/^((?:Codon frequencies)|(?:Site-class models))\s*:\s+(.+)/) { - my ( $param, $val ) = ( $1, $2 ); - $self->{'_summary'}->{'inputparams'}->{$param} = $val; - } - elsif (/^\s+$/) { - next; - } - elsif ( /^ns\s+=\s+/ || /^Frequencies/ ) { - $self->_pushback($_); - last; - } - } -} - -sub _parse_codon_freqs { - my ($self) = @_; - my ( $okay, $done ) = ( 0, 0 ); - - while ( defined( $_ = $self->_readline ) ) { - if (/^Nei|\(A\) Nei/) { $self->_pushback($_); last } - last if ($done); - next if (/^\s+/); - next - unless ( $okay || /^Codon position x base \(3x4\) table\, overall/ ); - $okay = 1; - if (s/^position\s+(\d+):\s+//) { - my $pos = $1; - s/\s+$//; - my @bases = split; - foreach my $str (@bases) { - my ( $base, $freq ) = split( /:/, $str, 2 ); - $self->{'_summary'}->{'codonposition'}->[ $pos - 1 ]->{$base} = - $freq; - } - $done = 1 if $pos == 3; - } - } - $done = 0; - while ( defined( $_ = $self->_readline ) ) { - if (/^Nei\s\&\sGojobori|\(A\)\sNei-Gojobori/) { - $self->_pushback($_); - last; - } - last if ($done); - if (/^Codon frequencies under model, for use in evolver/) { - while ( defined( $_ = $self->_readline ) ) { - last if (/^\s+$/); - s/^\s+//; - s/\s+$//; - push @{ $self->{'_summary'}->{'codonfreqs'} }, [split]; - } - $done = 1; - } - } -} - -sub _parse_aa_freqs { - my ($self) = @_; - my ( $okay, $done, $header ) = ( 0, 0, 0 ); - my (@bases); - my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; - while ( defined( $_ = $self->_readline ) ) { - if ( /^TREE/ || /^AA distances/ ) { - $self->_pushback($_); - last; - } - last if ($done); - next if ( /^\s+$/ || /^\(Ambiguity/ ); - if (/^Frequencies\./) { - $okay = 1; - } - elsif ( !$okay ) { # skip till we see 'Frequencies. - next; - } - elsif ( !$header ) { - s/^\s+//; # remove leading whitespace - @bases = split; # get an array of the all the aa names - $header = 1; - $self->{'_summary'}->{'aafreqs'} = {}; # reset/clear values - next; - } - elsif ( - /^\#\s+constant\s+sites\:\s+ - (\d+)\s+ # constant sites - \(\s*([\d\.]+)\s*\%\s*\)/x - ) - { - $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; - $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; - } - elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) { - $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; - $done = 1; # done for sure - } - else { - my ( $seqname, @freqs ) = split; - my $basect = 0; - foreach my $f (@freqs) { - - # this will also store 'Average' - $self->{'_summary'}->{'aafreqs'}->{$seqname} - ->{ $bases[ $basect++ ] } = $f; - } - } - } -} - -# This is for parsing the automatic tree output - -sub _parse_StarDecomposition { - my ($self) = @_; - my %data; - - return %data; -} - -sub _parse_aa_dists { - my ($self) = @_; - my ( $okay, $seen, $done ) = ( 0, 0, 0 ); - my ( %matrix, @names, @values ); - my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; - my $type = ''; - while ( defined( $_ = $self->_readline ) ) { - last if $done; - if (/^TREE/) { $self->_pushback($_); last; } - if (/^\s+$/) { - last if ($seen); - next; - } - if (/^(AA|ML) distances/) { - $okay = 1; - $type = $1; - next; - } - s/\s+$//g; # remove trailing space - if ($okay) { - my ( $seqname, @vl ) = split; - $seen = 1; - my $i = 0; - - # hacky workaround to problem with 3.14 aaml - if ( - $type eq 'ML' - && !@names - && # first entry - @vl - ) - { # not empty - push @names, $self->{'_summary'}->{'seqs'}->[0]->display_id; - } - for my $s (@names) { - last unless @vl; - $matrix{$seqname}->{$s} = $matrix{$s}->{$seqname} = shift @vl; - } - push @names, $seqname; - - $matrix{$seqname}->{$seqname} = 0; - } - $done = 1 if ( scalar @names == $numseqs ); - } - my %dist; - my $i = 0; - @values = (); - foreach my $lname (@names) { - my @row; - my $j = 0; - foreach my $rname (@names) { - my $v = $matrix{$lname}->{$rname}; - $v = $matrix{$rname}->{$lname} unless defined $v; - push @row, $v; - $dist{$lname}{$rname} = [ $i, $j++ ]; - } - $i++; - push @values, \@row; - } - return new Bio::Matrix::PhylipDist( - -program => $self->{'_summary'}->{'seqtype'}, - -matrix => \%dist, - -names => \@names, - -values => \@values - ); -} - -sub _parse_patterns { - my ($self) = @_; - my ( $patternct, @patterns, $ns, $ls ); - return if exists $self->{'_summary'}->{'patterns'}; - - while ( defined( $_ = $self->_readline ) ) { - if ( /^Codon\s+(usage|position)/ || /Model/ ) { - $self->_pushback($_); - last; - } - elsif ($patternct) { - - # last unless ( @patterns == $patternct ); - last if (/^\s+$/); - s/^\s+//; - push @patterns, split; - } - elsif (/^ns\s+\=\s*(\d+)\s+ls\s+\=\s*(\d+)/) { - ( $ns, $ls ) = ( $1, $2 ); - } - elsif (/^\# site patterns \=\s*(\d+)/) { - $patternct = $1; - } - else { - - # $self->debug("Unknown line: $_"); - } - } - $self->{'_summary'}->{'patterns'} = { - -patterns => \@patterns, - -ns => $ns, - -ls => $ls - }; -} - -sub _parse_seqs { - - # this should in fact be packed into a Bio::SimpleAlign object instead of - # an array but we'll stay with this for now - my ($self) = @_; - - # Use this flag to deal with paml 4 vs 3 differences - # In PAML 4 the sequences precede the CODONML|BASEML|AAML - # while in PAML3 the files start off with this - return 1 if $self->{'_already_parsed_seqs'}; - my ( @firstseq, @seqs ); - while ( defined( $_ = $self->_readline ) ) { - if (/^(Printing|After|TREE|Codon)/) { - $self->_pushback($_); - last; - } - last if ( /^\s+$/ && @seqs > 0 ); - next if (/^\s+$/); - next if (/^\d+\s+$/); - - # we are reading PHYLIP format - my ( $name, $seqstr ) = split( /\s+/, $_, 2 ); - $seqstr =~ s/\s+//g; # remove whitespace - unless (@firstseq) { - @firstseq = split( //, $seqstr ); - push @seqs, - Bio::LocatableSeq->new( - -display_id => $name, - -seq => $seqstr - ); - } - else { - - my $i = 0; - my $v; - while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { - - # replace the '.' with the correct seq from the - substr( $seqstr, $v, 1, $firstseq[$v] ); - $i = $v; - } - push @seqs, - Bio::LocatableSeq->new( - -display_id => $name, - -seq => $seqstr - ); - } - } - if ( @seqs > 0 ) { - $self->{'_summary'}->{'seqs'} = \@seqs; - $self->{'_already_parsed_seqs'} = 1; - } - 1; -} - -sub _parse_codoncts { } - -sub _parse_distmat { - my ($self) = @_; - my @results; - my $ver = 3.14; - my $firstseq, my $secondseq; - - while ( defined( $_ = $self->_readline ) ) { - next if /^\s+$/; - - # We need to get the names of the sequences if this is from YN00: - if (/^\(A\)\sNei-Gojobori\s\(1986\)\smethod/) { - $ver = 3.15; - while ( defined( $_ = $self->_readline ) ) { - if ($_ =~ m/.*\d+?\.\d+?\s*\(.*/) { - $secondseq = $_; - last; - } - $firstseq = $_; - } - } - last; - } - - #return unless (/^Nei\s*\&\s*Gojobori/); - - # skip the next 3 lines - if ( $self->{'_summary'}->{'seqtype'} eq 'CODONML' ) { - $self->_readline; - $self->_readline; - $self->_readline; - } - my $seqct = 0; - my @seqs; - if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { - if ($firstseq) { - $firstseq =~ s/(.+?)\s+.*/$1/; - $secondseq =~ s/(.+?)\s+.*/$1/; - chomp $firstseq; - chomp $secondseq; - push @seqs, Bio::PrimarySeq->new( -display_id => $firstseq ); - push @seqs, Bio::PrimarySeq->new( -display_id => $secondseq ); - } - } - while ( defined( $_ = $self->_readline ) ) { - last if ( /^\s+$/ && exists $self->{'_summary'}->{'ngmatrix'} ); - next if ( /^\s+$/ || /^NOTE:/i ); - chomp; - - my ( $seq, $rest ); - if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { - ( $seq, $rest ) = split( /\s+/, $_, 2 ); - } - else { - $_ =~ m/(.+?)\s*(-*\d+?\.\d+?.*)/; - $seq = $1; - $rest = $2; - } - $rest = '' unless defined $rest; # get rid of empty messages - my $j = 0; - if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' ) { - push @seqs, Bio::PrimarySeq->new( -display_id => $seq ); - } - while ($rest - && $rest =~ - /(\-?\d+(\.\d+)?)\s*\(\-?(\d+(\.\d+)?)\s+(\-?\d+(\.\d+)?)\)/g ) - { - $self->{'_summary'}->{'ngmatrix'}->[ $j++ ]->[$seqct] = { - 'omega' => $1, - 'dN' => $3, - 'dS' => $5 - }; - } - $seqct++; - } - if ( $self->{'_summary'}->{'seqtype'} eq 'YN00' && @seqs ) { - $self->{'_summary'}->{'seqs'} = \@seqs; - } - - 1; -} - -sub _parse_PairwiseCodon { - my ($self) = @_; - my @result; - my ( $a, $b, $log, $model, $t, $kappa, $omega, $fixedkappa ); - # check to see if we have a fixed kappa: - if ( $self->{'_summary'}->{'model'} =~ /kappa = (\d+?\.\d+?) fixed/) { - $fixedkappa = $1; - } - while ( defined( $_ = $self->_readline ) ) { - if (/^pairwise comparison, codon frequencies\:\s*(\S+)\./) { - $model = $1; - } - # 1st line of a pair block, e.g. - # 2 (all_c7259) ... 1 (all_s57600) - elsif (/^(\d+)\s+\((\S+)\)\s+\.\.\.\s+(\d+)\s+\((\S+)\)/) { - ( $a, $b ) = ( $1, $3 ); - } - # 2nd line of a pair block, e.g. - # lnL = -126.880601 - elsif (/^lnL\s+\=\s*(\-?\d+(\.\d+)?)/) { - $log = $1; - if ( defined( $_ = $self->_readline ) ) { - # 3rd line of a pair block, e.g. - # 0.19045 2.92330 0.10941 - s/^\s+//; - ( $t, $kappa, $omega ) = split; - # if there was a fixed kappa, there will only be two values here ($t, $omega) and $kappa = $fixedkappa. - if ($omega eq "") { - $omega = $kappa; - $kappa = $fixedkappa; - } - } - } - # 5th line of a pair block, e.g. - # t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353 - # OR lines like (note last field; this includes a fix for bug #3040) - # t= 0.0439 S= 0.0 N= 141.0 dN/dS= 0.1626 dN= 0.0146 dS= nan - elsif (m/^t\=\s*(\d+(\.\d+)?)\s+/) - { - # Breaking out each piece individually so that you can see - # what each regexp actually looks for - my $parse_string = $_; - $parse_string =~ m/.*t\s*\=\s*(\d+?\.\d+?)\s/; - my $temp_t = $1; - $parse_string =~ m/\sS\s*\=\s*(\d+?\.\d+?)\s/; - my $temp_S = $1; - $parse_string =~ m/\sN\s*\=\s*(\d+?\.\d+?)\s/; - my $temp_N = $1; - $parse_string =~ m/\sdN\/dS\s*\=\s*(\d+?\.\d+?)\s/; - my $temp_omega = $1; - $parse_string =~ m/\sdN\s*\=\s*(\d+?\.\d+?)\s/; - my $temp_dN = $1; - $parse_string =~ m/\sdS\s*\=\s*(.+)\s/; - my $temp_dS = $1; - $result[ $b - 1 ]->[ $a - 1 ] = { - 'lnL' => $log, - 't' => defined $t && length($t) ? $t : $temp_t, - 'S' => $temp_S, - 'N' => $temp_N, - 'kappa' => $kappa, - 'omega' => defined $omega && length($omega) ? $omega : $temp_omega, - 'dN' => $temp_dN, - 'dS' => $temp_dS - }; - } - # 4th line of a pair block (which is blank) - elsif (/^\s+$/) { - next; - } - elsif (/^\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)/) { - } - else { - $self->debug("unknown line: $_"); - } - } - return ( -mlmatrix => \@result ); -} - -sub _parse_YN_Pairwise { - my ($self) = @_; - my @result; - while ( defined( $_ = $self->_readline ) ) { - last if (/^seq\.\s+seq\./); - } - while ( defined( $_ = $self->_readline ) ) { - if ( - m/^\s+(\d+)\s+ # seq # - (\d+)\s+ # seq # - (\d+(\.\d+))\s+ # S - (\d+(\.\d+))\s+ # N - (\d+(\.\d+))\s+ # t - (\d+(\.\d+))\s+ # kappa - (\d+(\.\d+))\s+ # omega - \-??(\d+(\.\d+))\s+ # dN - \+\-\s+ - \-??(\d+(\.\d+))\s+ # dN SE - \-??(\d+(\.\d+))\s+ # dS - \+\-\s+ - \-??(\d+(\.\d+))\s+ # dS SE - /ox - ) - { - - $result[ $2 - 1 ]->[ $1 - 1 ] = { - 'S' => $3, - 'N' => $5, - 't' => $7, - 'kappa' => $9, - 'omega' => $11, - 'dN' => $13, - 'dN_SE' => $15, - 'dS' => $17, - 'dS_SE' => $19, - }; - } - elsif (/^\s+$/) { - next; - } - elsif (/^\(C\) LWL85, LPB93 & LWLm methods/) { - $self->_pushback($_); - last; - } - } - return ( -mlmatrix => \@result ); -} - -sub _parse_Forestry { - my ($self) = @_; - my ( $instancecount, $num_param, $loglikelihood, $score, $done, - $treelength ) = ( 0, 0, 0, 0, 0, 0 ); - my $okay = 0; - my ( @ids, %match, @branches, @trees ); - while ( defined( $_ = $self->_readline ) ) { - last if $done; - if (s/^TREE\s+\#\s*\d+:\s+//) { - ($score) = (s/MP\s+score\:\s+(\S+)\s+$//); - @ids = /(\d+)[\,\)]/g; - } - elsif (/^Node\s+\&/ - || /^\s+N37/ - || /^(CODONML|AAML|YN00|BASEML)/ - || /^\*\*/ - || /^Detailed output identifying parameters/ ) - { - $self->_pushback($_); - $done = 1; - last; - } - elsif (/^tree\s+length\s+\=\s+(\S+)/) { - $treelength = $1; # not going to store this for now - # as it is directly calculated from - # $tree->total_branch_length; - } - elsif (/^\s*lnL\(.+np\:\s*(\d+)\)\:\s+(\S+)/) { - - # elsif( /^\s*lnL\(.+\)\:\s+(\S+)/ ) { - ( $num_param, $loglikelihood ) = ( $1, $2 ); - } - elsif (/^\(/) { - s/([\,:])\s+/$1/g; - my $treestr = IO::String->new($_); - my $treeio = Bio::TreeIO->new( - -fh => $treestr, - -format => 'newick' - ); - my $tree = $treeio->next_tree; - if ($tree) { - $tree->score($loglikelihood); - $tree->id("num_param:$num_param"); - if ( $okay > 0 ) { - - # we don't save the trees with the number labels - if ( !%match && @ids ) { - my $i = 0; - for my $m (/([^():,]+):/g) { - $match{ shift @ids } = [$m]; - } - my %grp; - while ( my $br = shift @branches ) { - my ( $parent, $child ) = @$br; - if ( $match{$child} ) { - push @{ $match{$parent} }, @{ $match{$child} }; - } - else { - push @branches, $br; - } - } - if ( $self->verbose > 1 ) { - for my $k ( sort { $a <=> $b } keys %match ) { - $self->debug( "$k -> ", - join( ",", @{ $match{$k} } ), "\n" ); - } - } - } - - # Associate SEs to nodes using tags - if ( defined( $self->{_SEs} ) ) { - my @SEs = split( " ", $self->{_SEs} ); - my $i = 0; - foreach my $parent_id ( map { /\d+\.\.(\d+)/ } - split( " ", $self->{_branch_ids} ) ) - { - my @nodes; - my @node_ids = @{ $match{$parent_id} }; - my @nodes_L = - map { $tree->find_node( -id => $_ ) } @node_ids; - my $n = - @nodes_L < 2 - ? shift(@nodes_L) - : $tree->get_lca(@nodes_L); - if ( !$n ) { - $self->warn( -"no node could be found for node in SE assignation (no lca?)" - ); - } - $n->add_tag_value( 'SE', $SEs[$i] ); - $i++; - } - } - push @trees, $tree; - } - } - $okay++; - } - elsif (/^SEs for parameters/) { - my $se_line = $self->_readline; - $se_line =~ s/\n//; - $self->{_SEs} = $se_line; - } - elsif (/^\s*\d+\.\.\d+/) { - push @branches, map { [ split( /\.\./, $_ ) ] } split; - my $ids = $_; - $ids =~ s/\n//; - $self->{_branch_ids} = $ids; - } - } - return \@trees, \%match; -} - -sub _parse_NSsitesBatch { - my $self = shift; - my ( %data, $idlookup ); - my ( $okay, $done ) = ( 0, 0 ); - while ( defined( $_ = $self->_readline ) ) { - last if $done; - next if /^\s+$/; - next unless ( $okay || /^Model\s+\d+/ || /^TREE/ ); - - if (/^Model\s+(\d+)/) { - if ($okay) { - - # this only happens if $okay was already 1 and - # we hit a Model line - $self->_pushback($_); - $done = 1; - } - else { - chomp; - $data{'-model_num'} = $1; - ( $data{'-model_description'} ) = (/\:\s+(.+)/); - $okay = 1; - } - } - elsif (/^Time used\:\s+(\S+)/) { - $data{'-time_used'} = $1; - $done = 1; - } - elsif (/^kappa\s+\(ts\/tv\)\s+\=\s+(\S+)/) { - $data{'-kappa'} = $1; - } - elsif (/^TREE/) { - $self->_pushback($_); - ( $data{'-trees'}, $idlookup ) = $self->_parse_Forestry; - if ( defined $data{'-trees'} - && scalar @{ $data{'-trees'} } ) - { - $data{'-likelihood'} = $data{'-trees'}->[0]->score; - } - $okay = 1; - } - elsif (/^omega\s+\(dn\/ds\)\s+\=\s+(\S+)/i) { - - # for M0 (single ratio for the entire tree) - # explicitly put '1.00000' rather than '1', because \d+\.\d{5} - # is reported in all other cases. - my @p = (q/1.00000/); # since there is only one class, - my @w = $1; - $data{'-dnds_site_classes'} = { - 'p' => \@p, - 'w' => \@w - }; - - # since no K=X is provided, put 1 here - $data{q/-num_site_classes/} = 1; - } - elsif ( -/^(Naive Empirical Bayes)|(Bayes Empirical Bayes)|(Positively\sselected\ssites)/i - ) - { - $self->_pushback($_); - my ( $sites, $neb, $beb ) = $self->_parse_Pos_selected_sites; - $data{'-pos_sites'} = $sites; - $data{'-neb_sites'} = $neb; - $data{'-beb_sites'} = $beb; - } - elsif (/^dN/i) { - if (/K\=(\d+)/) { - $data{'-num_site_classes'} = $1; - while ( $_ = $self->_readline ) { - unless ( $_ =~ /^\s+$/ ) { - $self->_pushback($_); - last; - } - } - if (/^site class/) { - $self->_readline; - my $tmp = $self->_readline; - my @p = $tmp =~ /(\d+\.\d{5})/g; - $tmp = $self->_readline; - my @b_w = $tmp =~ /(\d+\.\d{5})/g; - $tmp = $self->_readline; - my @f_w = $tmp =~ /(\d+\.\d{5})/g; - my @w; - - foreach my $i ( 0 .. $#b_w ) { - push @w, - { - q/background/ => $b_w[$i], - q/foreground/ => $f_w[$i] - }; - } - $data{'-dnds_site_classes'} = { - q/p/ => \@p, - q/w/ => \@w - }; - } - else { - my $tmp = $self->_readline; - my @p = $tmp =~ /(\d+\.\d{5})/g; - $tmp = $self->_readline; - my @w = $tmp =~ /(\d+\.\d{5})/g; - $data{'-dnds_site_classes'} = { - 'p' => \@p, - 'w' => \@w - }; - } - } - elsif (/for each branch/) { - my %branch_dnds = $self->_parse_branch_dnds; - if ( !defined $data{'-trees'} ) { - $self->warn( - "No trees have been loaded, can't do anything\n"); - next; - } - my ($tree) = @{ $data{'-trees'} }; - if ( !$tree - || !ref($tree) - || !$tree->isa('Bio::Tree::Tree') ) - { - $self->warn("no tree object already stored!\n"); - next; - } - - # These need to be added to the Node/branches - while ( my ( $k, $v ) = each %branch_dnds ) { - - # we can probably do better by caching at some point - my @nodes; - for my $id ( split( /\.\./, $k ) ) { - my @nodes_L = - map { $tree->find_node( -id => $_ ) } - @{ $idlookup->{$id} }; - my $n = - @nodes_L < 2 - ? shift(@nodes_L) - : $tree->get_lca(@nodes_L); - if ( !$n ) { - $self->warn( - "no node could be found for $id (no lca?)"); - } - unless ( $n->is_Leaf && $n->id ) { - $n->id($id); - } - push @nodes, $n; - } - my ( $parent, $child ) = @nodes; - while ( my ( $kk, $vv ) = each %$v ) { - $child->add_tag_value( $kk, $vv ); - } - } - } - } - elsif (/^Parameters in beta:/) { - $_ = $self->_readline; # need the next line - if (/p\=\s+(\S+)\s+q\=\s+(\S+)/) { - $data{'-shape_params'} = { - 'shape' => 'beta', - 'p' => $1, - 'q' => $2 - }; - } - else { - $self->warn("unparseable beta parameters: $_"); - } - } - elsif (/^Parameters in beta\&w\>1:/) { - - # Parameters in beta&w>1: - # p0= 1.00000 p= 0.07642 q= 0.85550 - # (p1= 0.00000) w= 1.00000 - $_ = $self->_readline; # need the next line - my ( $p0, $p, $q, $p1, $w ); - if (/p0\=\s+(\S+)\s+p\=\s+(\S+)\s+q\=\s+(\S+)/) { - $p0 = $1; - $p = $2; - $q = $3; - } - else { - $self->warn("unparseable beta parameters: $_"); - } - $_ = $self->_readline; # need the next line - if (/\(p1\=\s+(\S+)\)\s+w\=\s*(\S+)/) { - $p1 = $1; - $w = $2; - $data{'-shape_params'} = { - 'shape' => 'beta', - 'p0' => $p0, - 'p' => $p, - 'q' => $q, - 'p1' => $p1, - 'w' => $w - }; - } - else { - $self->warn("unparseable beta parameters: $_"); - } - } - elsif (/^alpha\s+\(gamma\)\s+\=\s+(\S+)/) { - my $gamma = $1; - $_ = $self->_readline; - my ( @r, @f ); - if (s/^r\s+\(\s*\d+\)\:\s+//) { - @r = split; - } - $_ = $self->_readline; - if (s/^f\s*\:\s+//) { - @f = split; - } - $data{'-shape_params'} = { - 'shape' => 'alpha', - 'gamma' => $gamma, - 'r' => \@r, - 'f' => \@f - }; - } - } - return new Bio::Tools::Phylo::PAML::ModelResult(%data); -} - -sub _parse_Pos_selected_sites { - my $self = shift; - my $okay = 0; - my (%sites) = ( - 'default' => [], - 'neb' => [], - 'beb' => [] - ); - my $type = 'default'; - while ( defined( $_ = $self->_readline ) ) { - next if ( /^\s+$/ || /^\s+Pr\(w\>1\)/ ); - if ( /^Time used/ || /^TREE/ ) { - $self->_pushback($_); - last; - } - if (/^Naive Empirical Bayes/i) { - $type = 'neb'; - } - elsif (/^Bayes Empirical Bayes/i) { - $type = 'beb'; - } - elsif (/^Positively selected sites/) { - $okay = 1; - } - elsif ( $okay - && /^\s+(\d+)\s+(\S+)\s+(\-?\d+(?:\.\d+)?)(\**)\s+(\-?\d+(?:\.\d+)?)\s+\+\-\s+(\-?\d+(?:\.\d+)?)/ - ) - { - my $signif = $4; - $signif = '' unless defined $signif; - push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5, $6 ]; - } - elsif ( $okay - && /^\s+(\d+)\s+(\S+)\s+(\-?\d*(?:.\d+))(\**)\s+(\-?\d+(?:\.\d+)?)/ - ) - { - my $signif = $4; - $signif = '' unless defined $signif; - push @{ $sites{$type} }, [ $1, $2, $3, $signif, $5 ]; - } - elsif ( $okay && /^\s+(\d+)\s+(\S)\s+([\d\.\-\+]+)(\**)/ ) { - my $signif = $4; - $signif = '' unless defined $signif; - push @{ $sites{$type} }, [ $1, $2, $3, $signif ]; - } - } - return ( $sites{'default'}, $sites{'neb'}, $sites{'beb'} ); -} - -sub _parse_branch_dnds { - my $self = shift; - my ($okay) = (0); - my %branch_dnds; - my @header; - while ( defined( $_ = $self->_readline ) ) { - next if (/^\s+$/); - next unless ( $okay || /^\s+branch\s+t/ ); - if (/^\s+branch\s+(.+)/) { - s/^\s+//; - @header = split( /\s+/, $_ ); - $okay = 1; - } - elsif (/^\s*(\d+\.\.\d+)/) { - my $branch = $1; - s/^\s+//; - my $i = 0; - - # fancyness just maps the header names like 't' or 'dN' - # into the hash so we get at the end of the day - # 't' => 0.067 - # 'dN'=> 0.001 - $branch_dnds{$branch} = { map { $header[ $i++ ] => $_ } split }; - } - else { - $self->_pushback($_); - last; - } - } - return %branch_dnds; -} - -#baseml stuff -sub _parse_nt_freqs { - my ($self) = @_; - my ( $okay, $done, $header ) = ( 0, 0, 0 ); - my (@bases); - my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; - while ( defined( $_ = $self->_readline ) ) { - if ( /^TREE/ || /^Distances/ ) { $self->_pushback($_); last } - last if ($done); - next if ( /^\s+$/ || /^\(Ambiguity/ ); - if (/^Frequencies\./) { - $okay = 1; - } - elsif ( !$okay ) { # skip till we see 'Frequencies. - next; - } - elsif ( !$header ) { - s/^\s+//; # remove leading whitespace - @bases = split; # get an array of the all the aa names - $header = 1; - $self->{'_summary'}->{'ntfreqs'} = {}; # reset/clear values - next; - } - elsif ( - /^\#\s+constant\s+sites\:\s+ - (\d+)\s+ # constant sites - \(\s*([\d\.]+)\s*\%\s*\)/ox - ) - { - $self->{'_summary'}->{'stats'}->{'constant_sites'} = $1; - $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2; - } - elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) { - $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1; - $done = 1; # done for sure - } - else { - my ( $seqname, @freqs ) = split; - my $basect = 0; - foreach my $f (@freqs) { - - # this will also store 'Average' - $self->{'_summary'}->{'ntfreqs'}->{$seqname} - ->{ $bases[ $basect++ ] } = $f; - } - } - } -} - -sub _parse_nt_dists { - my ($self) = @_; - my ( $okay, $seen, $done ) = ( 0, 0, 0 ); - my ( %matrix, @names ); - my $numseqs = scalar @{ $self->{'_summary'}->{'seqs'} || [] }; - my $type = ''; - while ( defined( $_ = $self->_readline ) ) { - if (/^TREE/) { $self->_pushback($_); last; } - last if $done; - next if (/^This matrix is not used in later/); - if (/^\s+$/) { - last if ($seen); - next; - } - if (/^Distances:(\S+)\s+\(([^\)]+)\)\s+\(alpha set at (\-?\d+\.\d+)\)/) - { - $okay = 1; - $type = $1; - next; - } - s/\s+$//g; # remove trailing space - if ($okay) { - my ( $seqname, $vl ) = split( /\s+/, $_, 2 ); - $seen = 1; - my $i = 0; - if ( defined $vl ) { - while ( $vl =~ /(\-?\d+\.\d+)\s*\(\s*(\-?\d+\.\d+)\s*\)\s*/g ) { - my ( $kappa, $alpha ) = ( $1, $2 ); - $matrix{$seqname}{ $names[$i] } = - $matrix{ $names[$i] }{$seqname} = [ $kappa, $alpha ]; - - $i++; - } - unless ($i) { - $self->warn("no matches for $vl\n"); - } - } - push @names, $seqname; - $matrix{$seqname}->{$seqname} = [ 0, 0 ]; - } - $done = 1 if ( scalar @names == $numseqs ); - } - my %dist; - my $i = 0; - my ( @kvalues, @avalues ); - foreach my $lname (@names) { - my ( @arow, @krow ); - my $j = 0; - foreach my $rname (@names) { - my $v = $matrix{$lname}{$rname}; - - push @krow, $v->[0]; # kappa values - push @arow, $v->[1]; # alpha - $dist{$lname}{$rname} = [ $i, $j++ ]; - } - $i++; - push @kvalues, \@krow; - push @avalues, \@arow; - } - return ( - Bio::Matrix::PhylipDist->new( - -program => $self->{'_summary'}->{'seqtype'}, - -matrix => \%dist, - -names => \@names, - -values => \@kvalues - ), - Bio::Matrix::PhylipDist->new( - -program => $self->{'_summary'}->{'seqtype'}, - -matrix => \%dist, - -names => \@names, - -values => \@avalues - ) - ); -} - -# BASEML -sub _parse_rate_parametes { - my $self = shift; - my (%rate_parameters); - while ( defined( $_ = $self->_readline ) ) { - if (/^Rate\s+parameters:\s+/) { - s/\s+$//; - $rate_parameters{'rate_parameters'} = [ split( /\s+/, $_ ) ]; - } - elsif (/^Base\s+frequencies:\s+/) { - s/\s+$//; - $rate_parameters{'base_frequencies'} = [ split( /\s+/, $_ ) ]; - } - elsif ( - m/^Rate\s+matrix\s+Q,\s+Average\s+Ts\/Tv\s+(\([^\)+]+\))?\s*\=\s+ - (\-?\d+\.\d+)/x - ) - { - $rate_parameters{'average_TsTv'} = $1; - while ( defined( $_ = $self->_readline ) ) { - - # short circuit - last if (/^\s+$/); - if (/^alpha/) { - $self->_pushback($_); - last; - } - s/^\s+//; - s/\s+$//; - push @{ $rate_parameters{'rate_matrix_Q'} }, [split]; - } - } - elsif (/^alpha\s+\(gamma,\s+K=\s*(\d+)\s*\)\s*\=\s*(\-?\d+\.\d+)/) { - $rate_parameters{'K'} = $1; - $rate_parameters{'alpha'} = $2; - } - elsif (s/^(r|f):\s+//) { - my ($p) = $1; - s/\s+$//; - $rate_parameters{$p} = [split]; - } - } -} - -# RST parsing -sub _parse_rst { - my ($self) = @_; - return unless $self->{'_dir'} && -d $self->{'_dir'} && -r $self->{'_dir'}; - - my $rstfile = File::Spec->catfile( $self->{'_dir'}, $RSTFILENAME ); - return unless -e $rstfile && !-z $rstfile; - my $rstio = Bio::Root::IO->new( -file => $rstfile ); - - # define whatever data structures you need to store the data - # key points are to reuse existing bioperl objs (like Bio::Seq) - # where appropriate - my ( @firstseq, @seqs, @trees, @per_site_prob ); - my $count; - while ( defined( $_ = $rstio->_readline ) ) { - - # implement the parsing here - if (/^TREE\s+\#\s+(\d+)/) { - while ( defined( $_ = $rstio->_readline ) ) { - if (/tree\s+with\s+node\s+labels\s+for/) { - my $tree = Bio::TreeIO->new( - -noclose => 1, - -fh => $rstio->_fh, - -format => 'newick' - )->next_tree; - - # cleanup leading/trailing whitespace - for my $n ( $tree->get_nodes ) { - my $id = $n->id; - $id =~ s/^\s+//; - $id =~ s/\s+$//; - $n->id($id); - if ( defined( my $blen = $n->branch_length ) ) { - $blen =~ s/^\s+//; - $blen =~ s/\s+$//; - $n->branch_length($blen); - } - } - push @trees, $tree; - last; - } - } - } - elsif (/^Prob\sof\sbest\scharacter\sat\seach\snode,\slisted\sby\ssite/) - { - $self->{'_rst'}->{'persite'} = []; - while ( defined( $_ = $rstio->_readline ) ) { - next if ( /^Site/i || /^\s+$/ ); - if (s/^\s+(\d+)\s+(\d+)\s+([^:]+)\s*:\s*(.+)//) { - my ( $sitenum, $freq, $extant, $ancestral ) = - ( $1, $2, $3, $4 ); - my ( @anc_site, @extant_site ); - @extant_site = {}; - while ( $extant =~ s/^([A-Z\-]{3})\s+\(([A-Z*])\)\s+//g ) { - push @extant_site, { 'codon' => $1, 'aa' => $2 }; - } - while ( - $ancestral =~ s/^([A-Z\-]{3})\s+([A-Z*])\s+ # codon AA - (\S+)\s+ # Prob - \(([A-Z*])\s+(\S+)\)\s*//xg # AA Prob - ) - { - push @anc_site, - { - 'codon' => $1, - 'aa' => $2, - 'prob' => $3, - 'Yang95_aa' => $4, - 'Yang95_aa_prob' => $5 - }; - } - - # saving persite - $self->{'_rst'}->{'persite'}->[$sitenum] = - [ @extant_site, @anc_site ]; - } - elsif (/^Summary\sof\schanges\salong\sbranches\./) { - last; - } - } - } - elsif (/^Check\sroot\sfor\sdirections\sof\schange\./ - || /^Summary\sof\schanges\salong\sbranches\./ ) - { - my ( @branches, @branch2node, $branch, $node ); - my $tree = $trees[-1]; - if ( !$tree ) { - $self->warn("No tree built before parsing Branch changes\n"); - last; - } - my @nodes = ( - map { $_->[0] } - sort { $a->[1] <=> $b->[1] } - map { [ $_, $_->id =~ /^(\d+)\_?/ ] } $tree->get_nodes - ); - unshift @nodes, - undef; # fake first node so that index will match nodeid - while ( defined( $_ = $rstio->_readline ) ) { - next if /^\s+$/; - if (m/^List\sof\sextant\sand\sreconstructed\ssequences/) { - $rstio->_pushback($_); - last; - } - elsif (/^Branch\s+(\d+):\s+(\d+)\.\.(\d+)\s+/) { - my ( $left, $right ); - ( $branch, $left, $right ) = ( $1, $2, $3 ); - ($node) = $nodes[$right]; - if ( !$node ) { - $self->warn( -"cannot find $right in $tree ($branch $left..$right)\n" - ); - last; - } - if (/\(n=\s*(\S+)\s+s=\s*(\S+)\)/) { - $node->add_tag_value( 'n', $1 ); - $node->add_tag_value( 's', $2 ); - } - $branch2node[$branch] = $right; - } - elsif ( - /^\s+(\d+)\s+([A-Z*])\s+(\S+)\s+\-\>\s+([A-Z*])\s+(\S+)?/) - { - my ( $site, $anc, $aprob, $derived, $dprob ) = - ( $1, $2, $3, $4, $5 ); - if ( !$node ) { - $self->warn("no branch line was previously parsed!"); - next; - } - my %c = ( - 'site' => $site, - 'anc_aa' => $anc, - 'anc_prob' => $aprob, - 'derived_aa' => $derived, - ); - $c{'derived_prob'} = $dprob if defined $dprob; - $node->add_tag_value( 'changes', \%c ); - } - } - } - elsif ( - /^Overall\s+accuracy\s+of\s+the\s+(\d+)\s+ancestral\s+sequences:/) - { - my $line = $rstio->_readline; - $line =~ s/^\s+//; - $line =~ s/\s+$//; - my @overall_site = split( /\s+/, $line ); - - # skip next 2 lines, want the third - for ( 1 .. 3 ) { - $line = $rstio->_readline; - } - $line =~ s/^\s+//; - $line =~ s/\s+$//; - my @overall_seq = split( /\s+/, $line ); - if ( @overall_seq != @overall_site - || @overall_seq != @seqs ) - { - $self->warn( - "out of sync somehow seqs, site scores don't match\n"); - $self->warn("@seqs @overall_seq @overall_site\n"); - } - for (@seqs) { - $_->description( - sprintf( - "overall_accuracy_site=%s overall_accuracy_seq=%s", - shift @overall_site, - shift @overall_seq - ) - ); - } - } - elsif (m/^List of extant and reconstructed sequences/o) { - my $seqcount = 0; - while ( defined( $_ = $rstio->_readline ) ) { - last if (/^Overall accuracy of the/); - if (/^\s+$/) { - last if $seqcount && $seqcount == @seqs; - next; - } - if (/^\s*(\d+)\s+(\d+)\s+$/) { $seqcount = $1; next } - - # runmode = (0) - # this should in fact be packed into a Bio::SimpleAlign object - # instead of an array but we'll stay with this for now - if (/^node/) { - my ( $name, $num, $seqstr ) = split( /\s+/, $_, 3 ); - $name .= $num; - $seqstr =~ s/\s+//g; # remove whitespace - unless (@firstseq) { - @firstseq = split( //, $seqstr ); - push @seqs, - Bio::LocatableSeq->new( - -display_id => $name, - -seq => $seqstr - ); - } - else { - my $i = 0; - my $v; - while ( ( $v = index( $seqstr, '.', $i ) ) >= $i ) { - - # replace the '.' with the correct seq from the - substr( $seqstr, $v, 1, $firstseq[$v] ); - $i = $v; - } - $self->debug("adding seq $seqstr\n"); - push @seqs, - Bio::LocatableSeq->new( - -display_id => $name, - -seq => $seqstr - ); - } - } - } - $self->{'_rst'}->{'rctrted_seqs'} = \@seqs; - } - else { - } - } - $self->{'_rst'}->{'trees'} = \@trees; - return; -} - -1; diff --git a/Bio/Tools/Phylo/PAML/Codeml.pm b/Bio/Tools/Phylo/PAML/Codeml.pm deleted file mode 100644 index ac2e02137..000000000 --- a/Bio/Tools/Phylo/PAML/Codeml.pm +++ /dev/null @@ -1,255 +0,0 @@ -# -# BioPerl module for Bio::Tools::Phylo::PAML::Codeml -# -# Cared for by Jason Stajich -# -# Copyright Jason Stajich, Aaron J Mackey -# -# You may distribute this module under the same terms as perl itself - -# POD documentation - main docs before the code - -=head1 NAME - -Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml. - -=head1 SYNOPSIS - - #!/usr/bin/perl -Tw - use strict; - - use Bio::Tools::Phylo::PAML::Codeml; - - # need to specify the output file name (or a fh) (defaults to - # -file => "codeml.mlc"); also, optionally, the directory in which - # the other result files (rst, 2ML.dS, etc) may be found (defaults - # to "./") - my $parser = new Bio::Tools::Phylo::PAML::Codeml::Parser - (-file => "./results/mlc", -dir => "./results/"); - - # get the first/next result; a Bio::[...]::Codeml::Result object - my $result = $parser->next_result(); - - # get the sequences used in the analysis; returns Bio::PrimarySeq - # objects (OTU = Operational Taxonomic Unit). - my @otus = $result->get_seqs(); - - # codon summary: codon usage of each sequence [ arrayref of { - # hashref of counts for each codon } for each sequence and the - # overall sum ], and positional nucleotide distribution [ arrayref - # of { hashref of frequencies for each nucleotide } for each - # sequence and overall frequencies ]. - - my ($codonusage, $ntdist) = $result->get_codon_summary(); - - # example manipulations of $codonusage and $ntdist: - printf "There were %d '%s' codons in the first seq (%s)\n", - $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id(); - printf "There were %d '%s' codons used in all the sequences\n", - $codonusage->[$#{$codonusage}]->{AAA}, 'AAA'; - printf "Nucleotide '%c' was present %g of the time in seq %s\n", - 'A', $ntdist->[1]->{A}, $otus[1]->id(); - - # get Nei & Gojobori dN/dS matrix: - my $NGmatrix = $result->get_NGmatrix(); - - # get ML-estimated dN/dS matrix, if calculated; this corresponds to - # the runmode = -2, pairwise comparison usage of codeml - my $MLmatrix = $result->get_MLmatrix(); - - # These matrices are length(@otu) x length(@otu) "strict lower - # triangle" 2D-matrices, which means that the diagonal and - # everything above it is undefined. Each of the defined cells is a - # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t", - # "S" and "N". If a ML matrix, "lnL" will also be defined. Any - # additional ML parameters estimated by the model will be in an - # array ref under "params"; it's up to the user to know which - # position corresponds to which parameter (since PAML doesn't label - # them, and we can't guess very well yet (a TODO I guess). - - printf "The omega ratio for sequences %s vs %s was: %g\n", - $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega}; - - # with a little work, these matrices could also be passed to - # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building - # method that accepts a matrix of "distances" (using the LOWTRI - # option): - my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ]; - - # for runmode's other than -2, get tree topology with estimated - # branch lengths; returns a Bio::Tree::TreeI-based tree object with - # added PAML parameters at each node - my $tree = $result->get_tree(); - for my $node ($tree->get_nodes()) { - # inspect the tree: the "t" (time) parameter is available via - # $node->branch_length(); all other branch-specific parameters - # ("omega", "dN", etc.) are available via $node->param('omega'); - } - - # get any general model parameters: kappa (the - # transition/transversion ratio), NSsites model parameters ("p0", - # "p1", "w0", "w1", etc.), etc. - my $params = $result->get_model_params(); - printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1}; - - # for NSsites models, obtain posterior probabilities for membership - # in each class for every position; probabilities correspond to - # classes w0, w1, ... etc. - my @probs = $result->get_posteriors(); - - # find, say, positively selected sites! - if ($params->{w2} > 1) { - for (my $i = 0; $i < @probs ; $i++) { - if ($probs[$i]->[2] > 0.5) { - # assumes model M1: three w's, w0, w1 and w2 (positive selection) - printf "position %d: (%g prob, %g omega, %g mean w)\n", - $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3]; - } - } - } else { print "No positive selection found!\n"; } - -=head1 DESCRIPTION - -This module is used to parse the output from the PAML program codeml. -You can use the Bio::Tools::Run::Phylo::Phylo::PAML::Codeml module to -actually run codeml; this module is only useful to parse the output. - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to -the Bioperl mailing list. Your participation is much appreciated. - - bioperl-l@bioperl.org - General discussion - http://bioperl.org/MailList.shtml - About the mailing lists - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via -email or the web: - - bioperl-bugs@bioperl.org - http://bioperl.org/bioperl-bugs/ - -=head1 AUTHOR - Jason Stajich, Aaron Mackey - -Email jason@bioperl.org -Email amackey@virginia.edu - -=head1 TODO - -This module should also be able to handle "codemlsites" batch -output... - -=head1 APPENDIX - -The rest of the documentation details each of the object methods. -Internal methods are usually preceded with a _ - -=cut - - -# Let the code begin... - - -package Bio::Tools::Phylo::PAML::Codeml; -use vars qw(@ISA); -use strict; - -# Object preamble - inherits from Bio::Root::Root - -use Bio::Root::Root; -use Bio::Root::IO; -use Bio::TreeIO; -use IO::String; - -@ISA = qw(Bio::Root::Root Bio::Root::IO ); - -=head2 new - - Title : new - Usage : my $obj = new Bio::Tools::Phylo::PAML::Codeml(); - Function: Builds a new Bio::Tools::Phylo::PAML::Codeml object - Returns : Bio::Tools::Phylo::PAML::Codeml - Args : - - -=cut - -sub new { - my($class,@args) = @_; - - my $self = $class->SUPER::new(@args); - $self->_initialize_io(@args); - $self->_parse_mlc(); - return $self; -} - -=head2 get_trees - - Title : get_trees - Usage : my @trees = $codemlparser->get_trees(); - Function: Returns a list of trees (if any) are in the output file - Returns : List of L objects - Args : none - - -=cut - -sub get_trees{ - my ($self) = @_; - - -} - -=head2 get_statistics - - Title : get_statistics - Usage : my $data = $codemlparser->get_statistics - Function: Retrieves the set of pairwise comparisons - Returns : Hash Reference keyed as 'seqname' -> 'seqname' -> 'datatype' - Args : none - - -=cut - -sub get_statistics { - my ($self) = @_; - - -} - - -# parse the mlc file - -sub _parse_mlc { - my ($self) = @_; - my %data; - while( defined( $_ = $self->_readline) ) { - print; - # Aaron this is where the parsing should begin - - # I'll do the Tree objects if you like - - # I'd do it by building an IO::String for the - # the tree data - # or does it make more sense to parse this out of a collection of - # files? - if( /^TREE/ ) { - # ... - while( defined($_ = $self->_readline) ) { - if( /^\(/) { - my $treestr = IO::String->new($_); - my $treeio = Bio::TreeIO->new(-fh => $treestr, - -format => 'newick'); - # this is very tenative here!! - push @{$self->{'_trees'}}, $treeio->next_tree; - } - } - } - } -} - -1; diff --git a/Bio/Tools/Phylo/PAML/ModelResult.pm b/Bio/Tools/Phylo/PAML/ModelResult.pm deleted file mode 100644 index 1d60a217e..000000000 --- a/Bio/Tools/Phylo/PAML/ModelResult.pm +++ /dev/null @@ -1,564 +0,0 @@ -# -# BioPerl module for Bio::Tools::Phylo::PAML::ModelResult -# -# Please direct questions and support issues to -# -# Cared for by Jason Stajich -# -# Copyright Jason Stajich -# -# You may distribute this module under the same terms as perl itself - -# POD documentation - main docs before the code - -=head1 NAME - -Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML - -=head1 SYNOPSIS - - # get a ModelResult from a PAML::Result object - use Bio::Tools::Phylo::PAML; - my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc'); - my $result = $paml->next_result; - foreach my $model ( $result->get_NSSite_results ) { - print $model->model_num, " ", $model->model_description, "\n"; - print $model->kappa, "\n"; - print $model->run_time, "\n"; -# if you are using PAML < 3.15 then only one place for POS sites - for my $sites ( $model->get_pos_selected_sites ) { - print join("\t",@$sites),"\n"; - } -# otherwise query NEB and BEB slots - for my $sites ( $model->get_NEB_pos_selected_sites ) { - print join("\t",@$sites),"\n"; - } - - for my $sites ( $model->get_BEB_pos_selected_sites ) { - print join("\t",@$sites),"\n"; - } - - } - -=head1 DESCRIPTION - -Describe the object here - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to -the Bioperl mailing list. Your participation is much appreciated. - - bioperl-l@bioperl.org - General discussion - http://bioperl.org/wiki/Mailing_lists - About the mailing lists - -=head2 Support - -Please direct usage questions or support issues to the mailing list: - -I - -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem -with code and data examples if at all possible. - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via -email or the web: - - https://github.com/bioperl/bioperl-live/issues - -=head1 AUTHOR - Jason Stajich - -Email jason@open-bio.org - -=head1 APPENDIX - -The rest of the documentation details each of the object methods. -Internal methods are usually preceded with a _ - -=cut - - -# Let the code begin... - - -package Bio::Tools::Phylo::PAML::ModelResult; -use strict; - -# Object preamble - inherits from Bio::Root::Root - - -use base qw(Bio::Root::Root); - -=head2 new - - Title : new - Usage : my $obj = Bio::Tools::Phylo::PAML::ModelResult->new(); - Function: Builds a new Bio::Tools::Phylo::PAML::ModelResult object - Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult - Args : -model_num => model number - -model_description => model description - -kappa => value of kappa - -time_used => amount of time - -pos_sites => arrayref of sites under positive selection - -neb_sites => arrayref of sites under positive selection (by NEB analysis) - -beb_sites => arrayref of sites under positive selection (by BEB analysis) - -trees => arrayref of tree(s) data for this model - -shape_params => hashref of parameters - ('shape' => 'alpha', - 'gamma' => $g, - 'r' => $r, - 'f' => $f - ) - OR - ( 'shape' => 'beta', - 'p' => $p, - 'q' => $q - ) - -likelihood => likelihood - -num_site_classes => number of site classes - -dnds_site_classes => hashref with two keys, 'p' and 'w' - which each point to an array, each - slot is for a different site class. - 'w' is for dN/dS and 'p' is probability - -=cut - -sub new { - my($class,@args) = @_; - - my $self = $class->SUPER::new(@args); - my ($modelnum,$modeldesc,$kappa, - $timeused,$trees, - $pos_sites,$neb_sites,$beb_sites, - $num_site_classes, $shape_params, - $dnds_classes, - $likelihood) = $self->_rearrange([qw(MODEL_NUM - MODEL_DESCRIPTION - KAPPA - TIME_USED - TREES - POS_SITES - NEB_SITES BEB_SITES - NUM_SITE_CLASSES - SHAPE_PARAMS - DNDS_SITE_CLASSES - LIKELIHOOD)], - @args); - if( $trees ) { - if(ref($trees) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize trees"); - } else { - foreach my $t ( @$trees ) { - $self->add_tree($t); - } - } - } - $self->{'_treeiterator'} = 0; - if( $pos_sites ) { - if(ref($pos_sites) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize pos_sites"); - } else { - foreach my $s ( @$pos_sites ) { - if( ref($s) !~ /ARRAY/i ) { - $self->warn("Need an array reference for each entry in the pos_sites object"); - next; - } - $self->add_pos_selected_site(@$s); - } - } - } - if( $beb_sites ) { - if(ref($beb_sites) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize beb_sites"); - } else { - foreach my $s ( @$beb_sites ) { - if( ref($s) !~ /ARRAY/i ) { - $self->warn("need an array ref for each entry in the beb_sites object"); - next; - } - $self->add_BEB_pos_selected_site(@$s); - } - } - } - if( $neb_sites ) { - if(ref($neb_sites) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize neb_sites"); - } else { - foreach my $s ( @$neb_sites ) { - if( ref($s) !~ /ARRAY/i ) { - $self->warn("need an array ref for each entry in the neb_sites object"); - next; - } - $self->add_NEB_pos_selected_site(@$s); - } - } - } - - defined $modelnum && $self->model_num($modelnum); - defined $modeldesc && $self->model_description($modeldesc); - defined $kappa && $self->kappa($kappa); - defined $timeused && $self->time_used($timeused); - defined $likelihood && $self->likelihood($likelihood); - - $self->num_site_classes($num_site_classes || 0); - if( defined $dnds_classes ) { - if( ref($dnds_classes) !~ /HASH/i || - ! defined $dnds_classes->{'p'} || - ! defined $dnds_classes->{'w'} ) { - $self->warn("-dnds_site_classes expects a hashref with keys p and w"); - } else { - $self->dnds_site_classes($dnds_classes); - } - } - if( defined $shape_params ) { - if( ref($shape_params) !~ /HASH/i ) { - $self->warn("-shape_params expects a hashref not $shape_params\n"); - } else { - $self->shape_params($shape_params); - } - } - return $self; -} - - -=head2 model_num - - Title : model_num - Usage : $obj->model_num($newval) - Function: Get/Set the Model number (0,1,2,3...) - Returns : value of model_num (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub model_num { - my $self = shift; - return $self->{'_num'} = shift if @_; - return $self->{'_num'}; -} - -=head2 model_description - - Title : model_description - Usage : $obj->model_description($newval) - Function: Get/Set the model description - This is something like 'one-ratio', 'neutral', 'selection' - Returns : value of description (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub model_description{ - my $self = shift; - return $self->{'_model_description'} = shift if @_; - return $self->{'_model_description'}; -} - -=head2 time_used - - Title : time_used - Usage : $obj->time_used($newval) - Function: Get/Set the time it took to run this analysis - Returns : value of time_used (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub time_used{ - my $self = shift; - return $self->{'_time_used'} = shift if @_; - return $self->{'_time_used'}; -} - -=head2 kappa - - Title : kappa - Usage : $obj->kappa($newval) - Function: Get/Set kappa (ts/tv) - Returns : value of kappa (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub kappa{ - my $self = shift; - return $self->{'_kappa'} = shift if @_; - return $self->{'_kappa'}; -} - -=head2 num_site_classes - - Title : num_site_classes - Usage : $obj->num_site_classes($newval) - Function: Get/Set the number of site classes for this model - Returns : value of num_site_classes (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub num_site_classes{ - my $self = shift; - return $self->{'_num_site_classes'} = shift if @_; - return $self->{'_num_site_classes'}; -} - -=head2 dnds_site_classes - - Title : dnds_site_classes - Usage : $obj->dnds_site_classes($newval) - Function: Get/Set dN/dS site classes, a hashref - with 2 keys, 'p' and 'w' which point to arrays - one slot for each site class. - Returns : value of dnds_site_classes (a hashref) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub dnds_site_classes{ - my $self = shift; - return $self->{'_dnds_site_classes'} = shift if @_; - return $self->{'_dnds_site_classes'}; -} - -=head2 get_pos_selected_sites - - Title : get_pos_selected_sites - Usage : my @sites = $modelresult->get_pos_selected_sites(); - Function: Get the sites which PAML has identified as under positive - selection (w > 1). This returns an array with each slot - being a site, 4 values, - site location (in the original alignment) - Amino acid (I *think* in the first sequence) - P (P value) - Significance (** indicated > 99%, * indicates >=95%) - Returns : Array - Args : none - - -=cut - -sub get_pos_selected_sites{ - return @{$_[0]->{'_posselsites'} || []}; -} - -=head2 add_pos_selected_site - - Title : add_pos_selected_site - Usage : $result->add_pos_selected_site($site,$aa,$pvalue,$signif); - Function: Add a site to the list of positively selected sites - Returns : count of the number of sites stored - Args : $site - site number (in the alignment) - $aa - amino acid under selection - $pvalue - float from 0->1 represent probability site is under selection according to this model - $signif - significance (coded as either empty, '*', or '**' - -=cut - -sub add_pos_selected_site{ - my ($self,$site,$aa,$pvalue,$signif) = @_; - push @{$self->{'_posselsites'}}, [ $site,$aa,$pvalue,$signif ]; - return scalar @{$self->{'_posselsites'}}; -} - -=head2 get_NEB_pos_selected_sites - - Title : get_NEB_pos_selected_sites - Usage : my @sites = $modelresult->get_NEB_pos_selected_sites(); - Function: Get the sites which PAML has identified as under positive - selection (w > 1) using Naive Empirical Bayes. - This returns an array with each slot being a site, 4 values, - site location (in the original alignment) - Amino acid (I *think* in the first sequence) - P (P value) - Significance (** indicated > 99%, * indicates > 95%) - post mean for w - Returns : Array - Args : none - - -=cut - -sub get_NEB_pos_selected_sites{ - return @{$_[0]->{'_NEBposselsites'} || []}; -} - -=head2 add_NEB_pos_selected_site - - Title : add_NEB_pos_selected_site - Usage : $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif); - Function: Add a site to the list of positively selected sites - Returns : count of the number of sites stored - Args : $site - site number (in the alignment) - $aa - amino acid under selection - $pvalue - float from 0->1 represent probability site is under selection according to this model - $signif - significance (coded as either empty, '*', or '**' - $postmean - post mean for w - -=cut - -sub add_NEB_pos_selected_site{ - my ($self,@args) = @_; - push @{$self->{'_NEBposselsites'}}, [ @args ]; - return scalar @{$self->{'_NEBposselsites'}}; -} - - - -=head2 get_BEB_pos_selected_sites - - Title : get_BEB_pos_selected_sites - Usage : my @sites = $modelresult->get_BEB_pos_selected_sites(); - Function: Get the sites which PAML has identified as under positive - selection (w > 1) using Bayes Empirical Bayes. - This returns an array with each slot being a site, 6 values, - site location (in the original alignment) - Amino acid (I *think* in the first sequence) - P (P value) - Significance (** indicated > 99%, * indicates > 95%) - post mean for w (mean) - Standard Error for w (SE) - Returns : Array - Args : none - -=cut - -sub get_BEB_pos_selected_sites{ - return @{$_[0]->{'_BEBposselsites'} || []}; -} - -=head2 add_BEB_pos_selected_site - - Title : add_BEB_pos_selected_site - Usage : $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif); - Function: Add a site to the list of positively selected sites - Returns : count of the number of sites stored - Args : $site - site number (in the alignment) - $aa - amino acid under selection - $pvalue - float from 0->1 represent probability site is under selection according to this model - $signif - significance (coded as either empty, '*', or '**' - $postmean - post mean for w - $SE - Standard Error for w - -=cut - -sub add_BEB_pos_selected_site{ - my ($self,@args) = @_; - push @{$self->{'_BEBposselsites'}}, [ @args ]; - return scalar @{$self->{'_BEBposselsites'}}; -} - -=head2 next_tree - - Title : next_tree - Usage : my $tree = $factory->next_tree; - Function: Get the next tree from the factory - Returns : L - Args : none - -=cut - -sub next_tree{ - my ($self,@args) = @_; - return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef; -} - -=head2 get_trees - - Title : get_trees - Usage : my @trees = $result->get_trees; - Function: Get all the parsed trees as an array - Returns : Array of trees - Args : none - - -=cut - -sub get_trees{ - my ($self) = @_; - return @{$self->{'_trees'} || []}; -} - -=head2 rewind_tree_iterator - - Title : rewind_tree_iterator - Usage : $result->rewind_tree_iterator() - Function: Rewinds the tree iterator so that next_tree can be - called again from the beginning - Returns : none - Args : none - -=cut - -sub rewind_tree_iterator { - shift->{'_treeiterator'} = 0; -} - -=head2 add_tree - - Title : add_tree - Usage : $result->add_tree($tree); - Function: Adds a tree - Returns : integer which is the number of trees stored - Args : L - -=cut - -sub add_tree{ - my ($self,$tree) = @_; - if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) { - push @{$self->{'_trees'}},$tree; - } - return scalar @{$self->{'_trees'}}; -} - -=head2 shape_params - - Title : shape_params - Usage : $obj->shape_params($newval) - Function: Get/Set shape params for the distribution, 'alpha', 'beta' - which is a hashref - with 1 keys, 'p' and 'q' - Returns : value of shape_params (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub shape_params{ - my $self = shift; - return $self->{'_shape_params'} = shift if @_; - return $self->{'_shape_params'}; -} - -=head2 likelihood - - Title : likelihood - Usage : $obj->likelihood($newval) - Function: log likelihood - Returns : value of likelihood (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub likelihood{ - my $self = shift; - return $self->{'likelihood'} = shift if @_; - return $self->{'likelihood'}; -} - -1; diff --git a/Bio/Tools/Phylo/PAML/Result.pm b/Bio/Tools/Phylo/PAML/Result.pm deleted file mode 100644 index 4aa52cb98..000000000 --- a/Bio/Tools/Phylo/PAML/Result.pm +++ /dev/null @@ -1,1238 +0,0 @@ -# -# BioPerl module for Bio::Tools::Phylo::PAML::Result -# -# Please direct questions and support issues to -# -# Cared for by Jason Stajich -# -# Copyright Jason Stajich, Aaron Mackey -# -# You may distribute this module under the same terms as perl itself - -# POD documentation - main docs before the code - -=head1 NAME - -Bio::Tools::Phylo::PAML::Result - A PAML result set object - -=head1 SYNOPSIS - - # see Bio::Tools::Phylo::PAML for example usage - use Bio::Tools::Phylo::PAML; - my $parser = Bio::Tools::Phylo::PAML->new - (-file => "./results/mlc", -dir => "./results/"); - - # get the first/next result; a Bio::Tools::Phylo::PAML::Result object, - # which isa Bio::SeqAnalysisResultI object. - my $result = $parser->next_result(); - - my @seqs = $result->get_seqs; - my %input_params = $result->get_input_parameters; - my @basfreq = $result->get_codon_pos_basefreq; - my $MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix - my $NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix - - - # for AAML runs - my $AAmatrix = $result->get_AADistMatrix; - my $AAMLmatrix = $result->get_AAMLDistMatrix; - - # if -dir contains an rst file get list of - # Bio::PrimarySeq ancestral state reconstructions of the sequences - my @rsts = $result->get_rst_seqs; - - - # if you want to print the changes on the tree - # this will print out the - # anc_aa => ANCESTRAL AMINO ACID - # anc_prob => ANCESTRAL AA PROBABILITY - # derived_aa => DERIVED AA - # derived_prob => DERIVE AA PROBABILITY (where appropriate - NA for extant/tip taxas) - # site => which codon site this in the alignment - @trees = $result->get_rst_trees; - for my $t ( @trees ) { - for my $node ( $t->get_nodes ) { - next unless $node->ancestor; # skip root node - my @changes = $node->get_tag_values('changes'); - my $chgstr = ''; - for my $c ( @changes ) { - for my $k ( sort keys %$c ) { - $chgstr .= "$k => $c->{$k} "; - } - $chgstr .= "\n\t"; - } - - printf "node:%s n=%s s=%s\n\t%s\n", - $node->id, - $node->get_tag_values('n'), - $node->get_tag_values('s'), - $chgstr; - } - } - - # Persite probabilities - my $persite = $result->get_rst_persite; - # let's score site 1 - $site = $persite->[2]; - # so site 2, node 2 (extant node, node 2) - print $site->[2]->{'codon'}, ' ',$site->[2]->{'aa'},"\n"; - # site 2, node 3 - print $site->[3]->{'codon'}, ' ',$site->[3]->{'aa'}, "\n"; - - # ancestral node 9, codon, aa, marginal probabilities; Yang95 is listed as - # (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650) in PAML rst file. - print $site->[9]->{'codon'}, ' ',$site->[9]->{'aa'}, ' ', $site->[9]->{'prob'}, ' ', - $site->[9]->{'Yang95_aa'},' ', $site->[9]->{'Yang95_aa_prob'},"\n"; - - -=head1 DESCRIPTION - -This is a container object for PAML Results. - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to -the Bioperl mailing list. Your participation is much appreciated. - - bioperl-l@bioperl.org - General discussion - http://bioperl.org/wiki/Mailing_lists - About the mailing lists - -=head2 Support - -Please direct usage questions or support issues to the mailing list: - -I - -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem -with code and data examples if at all possible. - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via -email or the web: - - https://github.com/bioperl/bioperl-live/issues - -=head1 AUTHOR - Jason Stajich, Aaron Mackey - - Email jason-at-bioperl-dot-org - Email amackey-at-virginia-dot-edu - -=head1 CONTRIBUTORS - -Albert Vilella avilella-AT-gmail-DOT-com - -=head1 APPENDIX - -The rest of the documentation details each of the object methods. -Internal methods are usually preceded with a _ - -=cut - - -# Let the code begin... - - -package Bio::Tools::Phylo::PAML::Result; -use strict; - - -use base qw(Bio::Root::Root Bio::AnalysisResultI); - -=head2 new - - Title : new - Usage : my $obj = Bio::Tools::Phylo::PAML::Result->new(%data); - Function: Builds a new Bio::Tools::Phylo::PAML::Result object - Returns : Bio::Tools::Phylo::PAML::Result - Args : -trees => array reference of Bio::Tree::TreeI objects - -MLmatrix => ML matrix - -seqs => array reference of Bio::PrimarySeqI objects - -codonpos => array reference of codon positions - -codonfreq => array reference of codon frequencies - -version => version string - -model => model string - -patterns => hashref with the fields '-patterns', '-ns', '-ls' - -stats => array ref of misc stats (optional) - -aafreq => Hashref of AA frequencies (only for AAML) - -aadistmat => Bio::Matrix::PhylipDist (only for AAML) - -aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML) - -ntfreq => array ref of NT frequencies (only for BASEML) - -seqfile => seqfile used - -kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML) - -alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML) - -NSSitesresult => arrayref of PAML::ModelResult - -input_params => input params from .ctl file - -rst => array reference of Bio::PrimarySeqI objects - of ancestral state reconstruction - -rst_persite=> arrayref of persite data, this is a complicated set of AoH - -rst_trees => rst trees with changes coded on the tree - -See Also: L, L, L, L - - -=cut - -sub new { - my($class,@args) = @_; - - my $self = $class->SUPER::new(@args); - my ($trees,$mlmat,$seqs,$ngmatrix, - $codonpos,$codonfreq,$version, - $model,$patterns, $stats, - $aafreq, $aadistmat, - $aamldistmat, - $ntfreqs, $seqfile, $kappa_mat, $alpha_mat, - $NSSitesresults,$input_params,$rst,$rst_persite,$rst_trees ) = - $self->_rearrange([qw - (TREES MLMATRIX - SEQS NGMATRIX - CODONPOS CODONFREQ - VERSION MODEL PATTERNS - STATS AAFREQ AADISTMAT - AAMLDISTMAT - NTFREQ SEQFILE - KAPPA_DISTMAT - ALPHA_DISTMAT - NSSITESRESULTS - INPUT_PARAMS - RST RST_PERSITE RST_TREES)], - @args); - $self->reset_seqs; - if( $trees ) { - if(ref($trees) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize trees"); - } else { - foreach my $t ( @$trees ) { - $self->add_tree($t); - } - } - } - $self->{'_treeiterator'} = 0; - - if( $mlmat ) { - if( ref($mlmat) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize MLmatrix"); - } else { - $self->set_MLmatrix($mlmat); - } - } - if( $seqs ) { - if( ref($seqs) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize seqs"); - } else { - foreach my $s ( @$seqs ) { - $self->add_seq($s); - } - } - } - if( $ngmatrix ) { - if( ref($ngmatrix) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize NGmatrix"); - } else { - $self->set_NGmatrix($ngmatrix); - } - } - if( $codonfreq ) { - if( ref($codonfreq) =~ /ARRAY/i ) { - $self->set_CodonFreqs($codonfreq); - } else { - $self->warn("Must provide a valid array reference to initialize codonfreq"); - } - } - - if( $codonpos ) { - if( ref($codonpos) !~ /ARRAY/i ) { - $self->warn("Must provide a valid array reference to initialize codonpos"); - } else { - $self->set_codon_pos_basefreq(@$codonpos); - } - } - - $self->version($version) if defined $version; - $self->seqfile($seqfile) if defined $seqfile; - $self->model($model) if defined $model; - if( defined $patterns ) { - if( ref($patterns) =~ /HASH/i ) { - $self->patterns($patterns); - } else { - $self->warn("Must provide a valid array reference to initialize patterns"); - } - } - - $self->{'_aafreqs'} = {}; - if( $aafreq ) { - if( ref($aafreq) =~ /HASH/i ) { - $self->set_AAFreqs($aafreq); - } else { - $self->warn("Must provide a valid hash reference to initialize aafreq"); - } - } - if( $stats ) { - if( ref($stats) =~ /HASH/i ) { - while( my ($stat,$val) = each %$stats) { - $self->add_stat($stat,$val); - } - } else { - $self->warn("Must provide a valid hash reference initialize stats"); - } - } - $self->set_AADistMatrix($aadistmat) if defined $aadistmat; - $self->set_AAMLDistMatrix($aamldistmat) if defined $aamldistmat; - - if( defined $NSSitesresults ) { - if( ref($NSSitesresults) !~ /ARRAY/i ) { - $self->warn("expected an arrayref for -NSSitesresults"); - } else { - foreach my $m ( @$NSSitesresults ) { - $self->add_NSSite_result($m); - } - } - } - - $self->{'_ntfreqs'} = {}; - if( $ntfreqs ) { - if( ref($ntfreqs) =~ /HASH/i ) { - $self->set_NTFreqs($ntfreqs); - } else { - $self->warn("Must provide a valid hash reference to initialize ntfreq"); - } - } - - if( $kappa_mat ) { - $self->set_KappaMatrix($kappa_mat); - } - if( $alpha_mat ) { - $self->set_AlphaMatrix($alpha_mat); - } - - if( $input_params ) { - if( ref($input_params) !~ /HASH/i ) { - $self->warn("Must provide a valid hash object for input_params\n"); - } else { - while( my ($p,$v) = each %$input_params ) { - $self->set_input_parameter($p,$v); - } - } - - } - $self->reset_rst_seqs; - if( $rst ) { - if( ref($rst) =~ /ARRAY/i ) { - for ( @$rst ) { - $self->add_rst_seq($_); - } - } else { - $self->warn("Need a valid array ref for -rst option\n"); - } - } - if( defined $rst_persite ) { - $self->set_rst_persite($rst_persite); - } - $self->reset_rst_trees; - if( $rst_trees ) { - if( ref($rst_trees) =~ /ARRAY/i ) { - for ( @$rst_trees ) { - $self->add_rst_tree($_); - } - } else { - $self->warn("Need a valid array ref for -rst_trees option\n"); - } - } - - return $self; -} - -=head2 next_tree - - Title : next_tree - Usage : my $tree = $factory->next_tree; - Function: Get the next tree from the factory - Returns : L - Args : none - -=cut - -sub next_tree{ - my ($self,@args) = @_; - return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef; -} - -=head2 get_trees - - Title : get_trees - Usage : my @trees = $result->get_trees; - Function: Get all the parsed trees as an array - Returns : Array of trees - Args : none - - -=cut - -sub get_trees{ - my ($self) = @_; - return @{$self->{'_trees'} || []}; -} - -=head2 rewind_tree_iterator - - Title : rewind_tree_iterator - Usage : $result->rewind_tree_iterator() - Function: Rewinds the tree iterator so that next_tree can be - called again from the beginning - Returns : none - Args : none - -=cut - -sub rewind_tree_iterator { - shift->{'_treeiterator'} = 0; -} - -=head2 add_tree - - Title : add_tree - Usage : $result->add_tree($tree); - Function: Adds a tree - Returns : integer which is the number of trees stored - Args : L - -=cut - -sub add_tree{ - my ($self,$tree) = @_; - if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) { - push @{$self->{'_trees'}},$tree; - } - return scalar @{$self->{'_trees'}}; -} - - -=head2 set_MLmatrix - - Title : set_MLmatrix - Usage : $result->set_MLmatrix($mat) - Function: Set the ML Matrix - Returns : none - Args : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is - lower triangle pairwise) - - -=cut - -sub set_MLmatrix{ - my ($self,$mat) = @_; - return unless ( defined $mat ); - if( ref($mat) !~ /ARRAY/i ) { - $self->warn("Did not provide a valid 2D Array reference for set_MLmatrix"); - return; - } - $self->{'_mlmatrix'} = $mat; -} - -=head2 get_MLmatrix - - Title : get_MLmatrix - Usage : my $mat = $result->get_MLmatrix() - Function: Get the ML matrix - Returns : 2D Array reference - Args : none - - -=cut - -sub get_MLmatrix{ - my ($self,@args) = @_; - return $self->{'_mlmatrix'}; -} - -=head2 set_NGmatrix - - Title : set_NGmatrix - Usage : $result->set_NGmatrix($mat) - Function: Set the Nei & Gojobori Matrix - Returns : none - Args : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is - lower triangle pairwise) - - -=cut - -sub set_NGmatrix{ - my ($self,$mat) = @_; - return unless ( defined $mat ); - if( ref($mat) !~ /ARRAY/i ) { - $self->warn("Did not provide a valid 2D Array reference for set_NGmatrix"); - return; - } - $self->{'_ngmatrix'} = $mat; -} - -=head2 get_NGmatrix - - Title : get_NGmatrix - Usage : my $mat = $result->get_NGmatrix() - Function: Get the Nei & Gojobori matrix - Returns : 2D Array reference - Args : none - - -=cut - -sub get_NGmatrix{ - my ($self,@args) = @_; - return $self->{'_ngmatrix'}; -} - - -=head2 add_seq - - Title : add_seq - Usage : $obj->add_seq($seq) - Function: Add a Bio::PrimarySeq to the Result - Returns : none - Args : Bio::PrimarySeqI -See also : L - -=cut - -sub add_seq{ - my ($self,$seq) = @_; - if( $seq ) { - unless( $seq->isa("Bio::PrimarySeqI") ) { - $self->warn("Must provide a valid Bio::PrimarySeqI to add_seq"); - return; - } - push @{$self->{'_seqs'}},$seq; - } - -} - -=head2 reset_seqs - - Title : reset_seqs - Usage : $result->reset_seqs - Function: Reset the OTU seqs stored - Returns : none - Args : none - - -=cut - -sub reset_seqs{ - my ($self) = @_; - $self->{'_seqs'} = []; -} - -=head2 get_seqs - - Title : get_seqs - Usage : my @otus = $result->get_seqs - Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit) - Returns : Array of Bio::PrimarySeq - Args : None -See also : L - -=cut - -sub get_seqs{ - my ($self) = @_; - return @{$self->{'_seqs'}}; -} - -=head2 set_codon_pos_basefreq - - Title : set_codon_pos_basefreq - Usage : $result->set_codon_pos_basefreq(@freqs) - Function: Set the codon position base frequencies - Returns : none - Args : Array of length 3 where each slot has a hashref - keyed on DNA base - - -=cut - -sub set_codon_pos_basefreq { - my ($self,@codonpos) = @_; - if( scalar @codonpos != 3 ) { - $self->warn("invalid array to set_codon_pos_basefreq, must be an array of length 3"); - return; - } - foreach my $pos ( @codonpos ) { - if( ref($pos) !~ /HASH/i || - ! exists $pos->{'A'} ) { - $self->warn("invalid array to set_codon_pos_basefreq, must be an array with hashreferences keyed on DNA bases, C,A,G,T"); - } - } - $self->{'_codonposbasefreq'} = [@codonpos]; -} - -=head2 get_codon_pos_basefreq - - Title : get_codon_pos_basefreq - Usage : my @basepos = $result->get_codon_pos_basefreq; - Function: Get the codon position base frequencies - Returns : Array of length 3 (each codon position), each - slot is a hashref keyed on DNA bases, the values are - the frequency of the base at that position for all sequences - Args : none - Note : The array starts at 0 so position '1' is in position '0' - of the array - -=cut - -sub get_codon_pos_basefreq{ - my ($self) = @_; - return @{$self->{'_codonposbasefreq'}}; -} - -=head2 version - - Title : version - Usage : $obj->version($newval) - Function: Get/Set version - Returns : value of version - Args : newvalue (optional) - - -=cut - -sub version{ - my $self = shift; - $self->{'_version'} = shift if @_; - return $self->{'_version'}; -} - -=head2 seqfile - - Title : seqfile - Usage : $obj->seqfile($newval) - Function: Get/Set seqfile - Returns : value of seqfile - Args : newvalue (optional) - - -=cut - -sub seqfile{ - my $self = shift; - $self->{'_seqfile'} = shift if @_; - return $self->{'_seqfile'}; -} - -=head2 model - - Title : model - Usage : $obj->model($newval) - Function: Get/Set model - Returns : value of model - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub model{ - my $self = shift; - - return $self->{'_model'} = shift if @_; - return $self->{'_model'}; -} - - -=head2 patterns - - Title : patterns - Usage : $obj->patterns($newval) - Function: Get/Set Patterns hash - Returns : Hashref of pattern data - Args : [optional] Hashref of patterns - : The hashref is typically - : { -patterns => \@arrayref - : -ns => $ns - : -ls => $ls - : } - -=cut - -sub patterns{ - my $self = shift; - return $self->{'_patterns'} = shift if @_; - return $self->{'_patterns'}; -} - -=head2 set_AAFreqs - - Title : set_AAFreqs - Usage : $result->set_AAFreqs(\%aafreqs); - Function: Get/Set AA freqs - Returns : none - Args : Hashref, keys are the sequence names, each points to a hashref - which in turn has keys which are the amino acids - - -=cut - -sub set_AAFreqs{ - my ($self,$aafreqs) = @_; - - if( $aafreqs && ref($aafreqs) =~ /HASH/i ) { - foreach my $seqname ( keys %{$aafreqs} ) { - $self->{'_aafreqs'}->{$seqname} = $aafreqs->{$seqname}; - } - } -} - -=head2 get_AAFreqs - - Title : get_AAFreqs - Usage : my %all_aa_freqs = $result->get_AAFreqs() - OR - my %seq_aa_freqs = $result->get_AAFreqs($seqname) - Function: Get the AA freqs, either for every sequence or just - for a specific sequence - The average aa freqs for the entire set are also available - for the sequence named 'Average' - Returns : Hashref - Args : (optional) sequence name to retrieve aa freqs for - - -=cut - -sub get_AAFreqs{ - my ($self,$seqname) = @_; - if( $seqname ) { - return $self->{'_aafreqs'}->{$seqname} || {}; - } else { - return $self->{'_aafreqs'}; - } -} - -=head2 set_NTFreqs - - Title : set_NTFreqs - Usage : $result->set_NTFreqs(\%aafreqs); - Function: Get/Set NT freqs - Returns : none - Args : Hashref, keys are the sequence names, each points to a hashref - which in turn has keys which are the amino acids - - -=cut - -sub set_NTFreqs{ - my ($self,$freqs) = @_; - - if( $freqs && ref($freqs) =~ /HASH/i ) { - foreach my $seqname ( keys %{$freqs} ) { - $self->{'_ntfreqs'}->{$seqname} = $freqs->{$seqname}; - } - } -} - -=head2 get_NTFreqs - - Title : get_NTFreqs - Usage : my %all_nt_freqs = $result->get_NTFreqs() - OR - my %seq_nt_freqs = $result->get_NTFreqs($seqname) - Function: Get the NT freqs, either for every sequence or just - for a specific sequence - The average nt freqs for the entire set are also available - for the sequence named 'Average' - Returns : Hashref - Args : (optional) sequence name to retrieve nt freqs for - - -=cut - -sub get_NTFreqs{ - my ($self,$seqname) = @_; - if( $seqname ) { - return $self->{'_ntfreqs'}->{$seqname} || {}; - } else { - return $self->{'_ntfreqs'}; - } -} - -=head2 add_stat - - Title : add_stat - Usage : $result->add_stat($stat,$value); - Function: Add some misc stat valuess (key/value pairs) - Returns : none - Args : $stat stat name - $value stat value - - -=cut - -sub add_stat{ - my ($self,$stat,$value) = @_; - return if( ! defined $stat || !defined $value ); - $self->{'_stats'}->{$stat} = $value; - return; -} - -=head2 get_stat - - Title : get_stat - Usage : my $value = $result->get_stat($name); - Function: Get the value for a stat of a given name - Returns : scalar value - Args : name of the stat - - -=cut - -sub get_stat{ - my ($self,$statname) = @_; - return $self->{'_stats'}->{$statname}; -} - -=head2 get_stat_names - - Title : get_stat_names - Usage : my @names = $result->get_stat_names; - Function: Get the stat names stored for the result - Returns : array of names - Args : none - - -=cut - -sub get_stat_names{ - my ($self) = @_; - return keys %{$self->{'_stats'} || {}}; -} - -=head2 get_AADistMatrix - - Title : get_AADistMatrix - Usage : my $mat = $obj->get_AADistMatrix() - Function: Get AADistance Matrix - Returns : value of AADistMatrix (Bio::Matrix::PhylipDist) - Args : none - - -=cut - -sub get_AADistMatrix{ - my $self = shift; - return $self->{'_AADistMatix'}; -} - -=head2 set_AADistMatrix - - Title : set_AADistMatrix - Usage : $obj->set_AADistMatrix($mat); - Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist) - Returns : none - Args : AADistrance Matrix (Bio::Matrix::PhylipDist) - - -=cut - -sub set_AADistMatrix{ - my ($self,$d) = @_; - if( ! $d || - ! ref($d) || - ! $d->isa('Bio::Matrix::PhylipDist') ) { - $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AADistMatrix"); - } - $self->{'_AADistMatix'} = $d; - return; -} - -=head2 get_AAMLDistMatrix - - Title : get_AAMLDistMatrix - Usage : my $mat = $obj->get_AAMLDistMatrix() - Function: Get AAMLDistance Matrix - Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist) - Args : none - - -=cut - -sub get_AAMLDistMatrix{ - my $self = shift; - return $self->{'_AAMLDistMatix'}; -} - -=head2 set_AAMLDistMatrix - - Title : set_AAMLDistMatrix - Usage : $obj->set_AAMLDistMatrix($mat); - Function: Set the AA ML Distrance Matrix (Bio::Matrix::PhylipDist) - Returns : none - Args : AAMLDistrance Matrix (Bio::Matrix::PhylipDist) - - -=cut - -sub set_AAMLDistMatrix{ - my ($self,$d) = @_; - if( ! $d || - ! ref($d) || - ! $d->isa('Bio::Matrix::PhylipDist') ) { - $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AAMLDistMatrix"); - } - $self->{'_AAMLDistMatix'} = $d; - return; -} - -=head2 add_NSSite_result - - Title : add_NSSite_result - Usage : $result->add_NSSite_result($model) - Function: Add a NSsite result (PAML::ModelResult) - Returns : none - Args : Bio::Tools::Phylo::PAML::ModelResult - - -=cut - -sub add_NSSite_result{ - my ($self,$model) = @_; - if( defined $model ) { - push @{$self->{'_nssiteresult'}}, $model; - } - return scalar @{$self->{'_nssiteresult'}}; -} - -=head2 get_NSSite_results - - Title : get_NSSite_results - Usage : my @results = @{$self->get_NSSite_results}; - Function: Get the reference to the array of NSSite_results - Returns : Array of PAML::ModelResult results - Args : none - - -=cut - -sub get_NSSite_results{ - my ($self) = @_; - return @{$self->{'_nssiteresult'} || []}; -} - -=head2 set_CodonFreqs - - Title : set_CodonFreqs - Usage : $obj->set_CodonFreqs($newval) - Function: Get/Set the Codon Frequence table - Returns : value of set_CodonFreqs (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub set_CodonFreqs{ - my $self = shift; - - return $self->{'_codonfreqs'} = shift if @_; - return $self->{'_codonfreqs'}; -} - -=head2 get_CodonFreqs - - Title : get_CodonFreqs - Usage : my @codon_freqs = $result->get_CodonFreqs() - Function: Get the Codon freqs - Returns : Array - Args : none - - -=cut - -sub get_CodonFreqs{ - my ($self) = @_; - return @{$self->{'_codonfreqs'} || []}; -} - - -=head2 BASEML Relevant values - -=cut - -=head2 get_KappaMatrix - - Title : get_KappaMatrix - Usage : my $mat = $obj->get_KappaMatrix() - Function: Get KappaDistance Matrix - Returns : value of KappaMatrix (Bio::Matrix::PhylipDist) - Args : none - - -=cut - -sub get_KappaMatrix{ - my $self = shift; - return $self->{'_KappaMatix'}; -} - -=head2 set_KappaMatrix - - Title : set_KappaMatrix - Usage : $obj->set_KappaMatrix($mat); - Function: Set the KappaDistrance Matrix (Bio::Matrix::PhylipDist) - Returns : none - Args : KappaDistrance Matrix (Bio::Matrix::PhylipDist) - - -=cut - -sub set_KappaMatrix{ - my ($self,$d) = @_; - if( ! $d || - ! ref($d) || - ! $d->isa('Bio::Matrix::PhylipDist') ) { - $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix"); - } - $self->{'_KappaMatix'} = $d; - return; -} - - -=head2 get_AlphaMatrix - - Title : get_AlphaMatrix - Usage : my $mat = $obj->get_AlphaMatrix() - Function: Get AlphaDistance Matrix - Returns : value of AlphaMatrix (Bio::Matrix::PhylipDist) - Args : none - - -=cut - -sub get_AlphaMatrix{ - my $self = shift; - return $self->{'_AlphaMatix'}; -} - -=head2 set_AlphaMatrix - - Title : set_AlphaMatrix - Usage : $obj->set_AlphaMatrix($mat); - Function: Set the AlphaDistrance Matrix (Bio::Matrix::PhylipDist) - Returns : none - Args : AlphaDistrance Matrix (Bio::Matrix::PhylipDist) - - -=cut - -sub set_AlphaMatrix{ - my ($self,$d) = @_; - if( ! $d || - ! ref($d) || - ! $d->isa('Bio::Matrix::PhylipDist') ) { - $self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix"); - } - $self->{'_AlphaMatix'} = $d; - return; -} - -=head2 set_input_parameter - - Title : set_input_parameter - Usage : $obj->set_input_parameter($p,$vl); - Function: Set an Input Parameter - Returns : none - Args : $parameter and $value - - -=cut - -sub set_input_parameter{ - my ($self,$p,$v) = @_; - return unless defined $p; - $self->{'_input_parameters'}->{$p} = $v; -} - -=head2 get_input_parameters - - Title : get_input_parameters - Usage : $obj->get_input_parameters; - Function: Get Input Parameters - Returns : Hash of key/value pairs - Args : none - - -=cut - -sub get_input_parameters{ - my ($self) = @_; - return %{$self->{'_input_parameters'} || {}}; -} - -=head2 reset_input_parameters - - Title : reset_input_parameters - Usage : $obj->reset_input_parameters; - Function: Reset the Input Parameters hash - Returns : none - Args : none - - -=cut - -sub reset_input_parameters{ - my ($self) = @_; - $self->{'_input_parameters'} = {}; -} - -=head1 Reconstructed Ancestral State relevant options - -=head2 add_rst_seq - - Title : add_rst_seq - Usage : $obj->add_rst_seq($seq) - Function: Add a Bio::PrimarySeq to the RST Result - Returns : none - Args : Bio::PrimarySeqI -See also : L - -=cut - -sub add_rst_seq{ - my ($self,$seq) = @_; - if( $seq ) { - unless( $seq->isa("Bio::PrimarySeqI") ) { - $self->warn("Must provide a valid Bio::PrimarySeqI to add_rst_seq"); - return; - } - push @{$self->{'_rstseqs'}},$seq; - } - -} - -=head2 reset_rst_seqs - - Title : reset_rst_seqs - Usage : $result->reset_rst_seqs - Function: Reset the RST seqs stored - Returns : none - Args : none - - -=cut - -sub reset_rst_seqs{ - my ($self) = @_; - $self->{'_rstseqs'} = []; -} - -=head2 get_rst_seqs - - Title : get_rst_seqs - Usage : my @otus = $result->get_rst_seqs - Function: Get the seqs Bio::PrimarySeq - Returns : Array of Bio::PrimarySeqI objects - Args : None -See also : L - -=cut - -sub get_rst_seqs{ - my ($self) = @_; - return @{$self->{'_rstseqs'} || []}; -} - - -=head2 add_rst_tree - - Title : add_rst_tree - Usage : $obj->add_rst_tree($tree) - Function: Add a Bio::Tree::TreeI to the RST Result - Returns : none - Args : Bio::Tree::TreeI -See also : L - -=cut - -sub add_rst_tree{ - my ($self,$tree) = @_; - if( $tree ) { - unless( $tree->isa("Bio::Tree::TreeI") ) { - $self->warn("Must provide a valid Bio::Tree::TreeI to add_rst_tree not $tree"); - return; - } - push @{$self->{'_rsttrees'}},$tree; - } -} - -=head2 reset_rst_trees - - Title : reset_rst_trees - Usage : $result->reset_rst_trees - Function: Reset the RST trees stored - Returns : none - Args : none - - -=cut - -sub reset_rst_trees{ - my ($self) = @_; - $self->{'_rsttrees'} = []; -} - -=head2 get_rst_trees - - Title : get_rst_trees - Usage : my @otus = $result->get_rst_trees - Function: Get the trees Bio::Tree::TreeI - Returns : Array of Bio::Tree::TreeI objects - Args : None -See also : L - -=cut - -sub get_rst_trees{ - my ($self) = @_; - return @{$self->{'_rsttrees'} || []}; -} - -=head2 set_rst_persite - - Title : set_rst_persite - Usage : $obj->set_rst_persite($newval) - Function: Get/Set the per-site RST values - Returns : value of set_rst_persite (a scalar) - Args : on set, new value (a scalar or undef, optional) - - -=cut - -sub set_rst_persite{ - my $self = shift; - - return $self->{'_rstpersite'} = shift if @_; - return $self->{'_rstpersite'}; -} - -=head2 get_rst_persite - - Title : get_rst_persite - Usage : my @rst_persite = @{$result->get_rst_persite()} - Function: Get the per-site RST values - Returns : Array - Args : none - - -=cut - -sub get_rst_persite{ - my ($self) = @_; - return $self->{'_rstpersite'} || []; -} - - - -1; diff --git a/scripts/utilities/bp_pairwise_kaks.pl b/scripts/utilities/bp_pairwise_kaks.pl deleted file mode 100644 index 0a05a8726..000000000 --- a/scripts/utilities/bp_pairwise_kaks.pl +++ /dev/null @@ -1,211 +0,0 @@ -#!perl -use strict; -use warnings; -# Author Jason Stajich - -=head1 NAME - -bp_pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences - -=head1 SYNOPSIS - -bp_pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-msa tcoffee/clustal] [-kaks yn00/codeml] - -=head1 DESCRIPTION - - This script will take as input a dataset of cDNA sequences verify - that they contain no stop codons, align them in protein space, - project the alignment back into cDNA and estimate the Ka - (non-synonymous) and Ks (synonymous) substitutions based on the ML - method of Yang with the PAML package. - - Requires: - * bioperl-run package - * PAML program codeml or yn00 - * Multiple sequence alignment programs Clustalw OR T-Coffee - - Often there are specific specific parameters you want to run when you - a computing Ka/Ks ratios so consider this script a starting point and - do not rely it on for every situation. - -=head1 FEEDBACK - -=head2 Mailing Lists - -User feedback is an integral part of the evolution of this and other -Bioperl modules. Send your comments and suggestions preferably to -the Bioperl mailing list. Your participation is much appreciated. - - bioperl-l@bioperl.org - General discussion - http://bioperl.org/wiki/Mailing_lists - About the mailing lists - -=head2 Reporting Bugs - -Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via the -web: - - https://github.com/bioperl/bioperl-live/issues - -=head1 AUTHOR - - Jason Stajich jason-at-bioperl-dot-org - -=cut - -eval { - # Ka/Ks estimators - require Bio::Tools::Run::Phylo::PAML::Codeml; - require Bio::Tools::Run::Phylo::PAML::Yn00; - - # Multiple Sequence Alignment programs - require Bio::Tools::Run::Alignment::Clustalw; - require Bio::Tools::Run::Alignment::TCoffee; -}; -if( $@ ) { - die("Must have bioperl-run pkg installed to run this script"); -} -# for projecting alignments from protein to R/DNA space -use Bio::Align::Utilities qw(aa_to_dna_aln); - -# for input of the sequence data -use Bio::SeqIO; -use Bio::AlignIO; - -# for the command line argument parsing -use Getopt::Long; - -my ($aln_prog, $kaks_prog,$format, $output, - $cdna,$verbose,$help) = qw(clustalw codeml fasta); - -GetOptions( - 'i|input:s' => \$cdna, - 'o|output:s' => \$output, - 'f|format:s' => \$format, - 'msa:s' => \$aln_prog, - 'kaks:s' => \$kaks_prog, - 'v|verbose' => \$verbose, - 'h|help' => \$help, - ); - -if( $help ) { - exec('perldoc',$0); - exit(0); -} -$verbose = -1 unless $verbose; -my ($aln_factory,$kaks_factory); -if( $aln_prog =~ /clus/i ) { - $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(-verbose => $verbose); -} elsif( $aln_prog =~ /t\_?cof/i ) { - $aln_factory = Bio::Tools::Run::Alignment::TCoffee->new(-verbose => $verbose); -} else { - warn("Did not provide either 'clustalw' or 'tcoffee' as alignment program names"); - exit(0); -} -unless( $aln_factory->executable ) { - warn("Could not find the executable for $aln_prog, make sure you have installed it and have either set ".uc($aln_prog)."DIR or it is in your PATH"); - exit(0); -} - - -if( $kaks_prog =~ /yn00/i ) { - $kaks_factory = Bio::Tools::Run::Phylo::PAML::Yn00->new(-verbose => $verbose); -} elsif( $kaks_prog =~ /codeml/i ) { - # change the parameters here if you want to tweak your Codeml running! - $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new - (-verbose => $verbose, - -params => { 'runmode' => -2, - 'seqtype' => 1, - } - ); -} -unless ( $kaks_factory->executable ) { - warn("Could not find the executable for $kaks_prog, make sure you have installed it and you have defined PAMLDIR or it is in your PATH"); - exit(0); -} - -unless ( $cdna && -f $cdna && -r $cdna && ! -z $cdna ) { - warn("Did not specify a valid cDNA sequence file as input"); - exit(0); -} - -my $seqin = new Bio::SeqIO(-file => $cdna, - -format => $format); - -my %seqs; -my @prots; -while( my $seq = $seqin->next_seq ) { - $seqs{$seq->display_id} = $seq; - my $protein = $seq->translate(); - my $pseq = $protein->seq(); - - $pseq =~ s/\*$//; - if( $pseq =~ /\*/ ) { - warn("provided a cDNA (".$seq->display_id.") sequence with a stop codon, PAML will choke!"); - exit(0); - } - # Tcoffee can't handle '*' - $pseq =~ s/\*//g; - $protein->seq($pseq); - push @prots, $protein; -} -if( @prots < 2 ) { - warn("Need at least 2 cDNA sequences to proceed"); - exit(0); -} - -local * OUT; -if( $output ) { - open(OUT, ">$output") || die("cannot open output $output for writing"); -} else { - *OUT = *STDOUT; -} - -my $aa_aln = $aln_factory->align(\@prots); -my $dna_aln = &aa_to_dna_aln($aa_aln, \%seqs); - -my @each = $dna_aln->each_seq(); - - -$kaks_factory->alignment($dna_aln); - -my ($rc,$parser) = $kaks_factory->run(); -if( $rc <= 0 ) { - warn($kaks_factory->error_string,"\n"); - exit; -} -my $result = $parser->next_result; - -if ($result->version =~ m/3\.15/) { - warn("This script does not work with v3.15 of PAML! Please use 3.14 instead."); - exit(0); -} - -my $MLmatrix = $result->get_MLmatrix(); - -my @otus = $result->get_seqs(); - -my @pos = map { - my $c= 1; - foreach my $s ( @each ) { - last if( $s->display_id eq $_->display_id ); - $c++; - } - $c; -} @otus; - -print OUT join("\t", qw(SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID)), "\n"; -for( my $i = 0; $i < (scalar @otus -1) ; $i++) { - for( my $j = $i+1; $j < (scalar @otus); $j++ ) { - my $sub_aa_aln = $aa_aln->select_noncont($pos[$i],$pos[$j]); - my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]); - print OUT join("\t", - $otus[$i]->display_id, - $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'}, - $MLmatrix->[$i]->[$j]->{'dS'}, - $MLmatrix->[$i]->[$j]->{'omega'}, - sprintf("%.2f",$sub_aa_aln->percentage_identity), - sprintf("%.2f",$sub_dna_aln->percentage_identity), - ), "\n"; - } -} diff --git a/t/Tools/Phylo/PAML.t b/t/Tools/Phylo/PAML.t deleted file mode 100644 index 21f7668f3..000000000 --- a/t/Tools/Phylo/PAML.t +++ /dev/null @@ -1,545 +0,0 @@ -# -*-Perl-*- Test Harness script for Bioperl -# $Id$ - -use strict; - -BEGIN { - use lib '.'; - use Bio::Root::Test; - - test_begin(-tests => 256, - -requires_module => 'IO::String'); - - use_ok('Bio::Tools::Phylo::PAML'); -} - -my $inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml.mlc')); -ok($inpaml); -my $result = $inpaml->next_result; -ok($result); -is($result->model, 'several dN/dS ratios for branches'); -like($result->version, qr'3\.12'); -my $MLmat = $result->get_MLmatrix; -my $NGmat = $result->get_NGmatrix; - -is($NGmat->[0]->[1]->{'omega'}, 0.2507); -is($NGmat->[0]->[1]->{'dN'}, 0.0863); -is($NGmat->[0]->[1]->{'dS'}, 0.3443); - -is($NGmat->[2]->[3]->{'omega'}, 0.2178); -is($NGmat->[2]->[3]->{'dN'}, 0.1348); -is($NGmat->[2]->[3]->{'dS'}, 0.6187); - -is($MLmat->[0]->[1]->{'omega'}, 0.19479); -is($MLmat->[0]->[1]->{'dN'}, 0.0839); -is($MLmat->[0]->[1]->{'dS'}, 0.4309); -is($MLmat->[0]->[1]->{'lnL'}, -1508.607268); -is($MLmat->[0]->[1]->{'t'}, 0.47825); -is($MLmat->[0]->[1]->{'kappa'}, 2.29137); - -is($MLmat->[2]->[3]->{'omega'}, 0.16114); -is($MLmat->[2]->[3]->{'dN'}, 0.1306); -is($MLmat->[2]->[3]->{'dS'}, 0.8105); -is($MLmat->[2]->[3]->{'lnL'},-1666.440696); -is($MLmat->[2]->[3]->{'t'}, 0.85281); -is($MLmat->[2]->[3]->{'kappa'}, 2.21652); - -my @codonposfreq = $result->get_codon_pos_basefreq(); -is($codonposfreq[0]->{'A'}, 0.23579); -is($codonposfreq[0]->{'T'}, 0.14737); -is($codonposfreq[1]->{'C'}, 0.25123); -is($codonposfreq[2]->{'G'}, 0.32842); - -# AAML parsing - Empirical model -$inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('aaml.mlc')); - -ok($inpaml); -$result = $inpaml->next_result; -ok($result); -is($result->model, 'Empirical (wag.dat)'); -my @trees = $result->get_trees; -is(@trees, 1); -is($trees[0]->score, -1042.768973); - -is((scalar grep { $_->is_Leaf } $trees[0]->get_nodes), $result->get_seqs); - -my $aadistmat = $result->get_AADistMatrix(); -ok($aadistmat); -is($aadistmat->get_entry('Cow', 'Horse'), 0.5462); -is($aadistmat->get_entry('Baboon', 'Langur'), 0.1077); - -my %aafreq = %{$result->get_AAFreqs()}; -ok(%aafreq); -is($aafreq{'Human'}->{'N'}, 0.0769); -is($aafreq{'Human'}->{'R'}, 0.1077); - -my %ratfreqs = %{$result->get_AAFreqs('Rat')}; -is($ratfreqs{'R'},0.0923); -is($ratfreqs{'F'},0.0154); -my %avgfreqs = %{$result->get_AAFreqs('Average')}; -is($avgfreqs{'Q'},0.0411); - -is($result->get_AAFreqs('Average')->{'I'},0.0424); - -my $patterns = $result->patterns; -my @pat = @{$patterns->{'-patterns'}}; -is(scalar @pat, 98); -is($patterns->{'-ns'}, 6); -is($patterns->{'-ls'}, 130); - -is((sort $result->get_stat_names)[0], 'constant_sites'); -is($result->get_stat('constant_sites'), 46); -is($result->get_stat('constant_sites_percentage'), 35.38); - -# AAML parsing - pairwise model -$inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('aaml_pairwise.mlc')); - -ok($inpaml); -$result = $inpaml->next_result; -ok($result); -is($result->model, 'Empirical_F (wag.dat)'); -is($result->get_stat('loglikelihood'),-1189.106658); -is($result->get_stat('constant_sites'), 170); -is($result->get_stat('constant_sites_percentage'), 59.65); - -is($result->get_AAFreqs('Average')->{'R'},0.0211); -is($result->get_AAFreqs('rabbit')->{'L'},0.1228); - -$aadistmat = $result->get_AADistMatrix(); -ok($aadistmat); -is($aadistmat->get_entry('rabbit', 'marsupial'), 0.2877); -is($aadistmat->get_entry('human', 'goat-cow'), 0.1439); - -$aadistmat = $result->get_AAMLDistMatrix(); -ok($aadistmat); -is($aadistmat->get_entry('rabbit', 'marsupial'), 0.3392); -is($aadistmat->get_entry('human', 'goat-cow'), 0.1551); - -my @seqs = $result->get_seqs; -is($seqs[0]->display_id, 'human'); - -# YN00 parsing, pairwise Ka/Ks from Yang & Nielsen 2000 -$inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('yn00.mlc')); - -ok($inpaml); -$result = $inpaml->next_result; - -ok($result); -$MLmat = $result->get_MLmatrix; -$NGmat = $result->get_NGmatrix; - -is($NGmat->[0]->[1]->{'omega'}, 0.251); -is($NGmat->[0]->[1]->{'dN'}, 0.0863); -is($NGmat->[0]->[1]->{'dS'}, 0.3443); -is($NGmat->[2]->[3]->{'omega'}, 0.218); -is($NGmat->[2]->[3]->{'dN'}, 0.1348); -is($NGmat->[2]->[3]->{'dS'}, 0.6187); - -is($MLmat->[0]->[1]->{'omega'}, 0.1625); -is($MLmat->[0]->[1]->{'dN'}, 0.0818); -is($MLmat->[0]->[1]->{'dS'}, 0.5031); -is($MLmat->[2]->[3]->{'omega'}, 0.1262); -is($MLmat->[2]->[3]->{'dN'}, 0.1298); -is($MLmat->[2]->[3]->{'dN_SE'}, 0.0149); -is($MLmat->[2]->[3]->{'dS'}, 1.0286); -is($MLmat->[2]->[3]->{'dS_SE'}, 0.2614); - -# codeml NSSites parsing - -$inpaml = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml_nssites.mlc')); - -ok($inpaml); -$result = $inpaml->next_result; - -ok($result); -is($result->model, 'One dN/dS ratio dGamma (ncatG=11)'); -is($result->version, 'paml 3.13, August 2002'); -$NGmat = $result->get_NGmatrix; -ok($NGmat); - -is($NGmat->[0]->[1]->{'omega'}, 0.2782); -is($NGmat->[0]->[1]->{'dN'}, 0.0133); -is($NGmat->[0]->[1]->{'dS'}, 0.0478); -is($NGmat->[1]->[2]->{'omega'}, 1.1055); -is($NGmat->[1]->[2]->{'dN'}, 0.0742); -is($NGmat->[1]->[2]->{'dS'}, 0.0671); - # this is - # model num description - # kappa log-likelihood tree length time used - # shape alpha/gamma r f -my @tstr = ([qw(0 one-ratio 0 - 4.54006 -906.017440 0.55764 - )], - [qw(1 neutral 2 - 4.29790 -902.503869 0.56529 - )], - [qw(2 selection 3 - 5.12250 -900.076500 0.6032 - )], - ); -my $iter = 0; -my $lastmodel; -foreach my $model ( $result->get_NSSite_results ) { - my $i = 0; - my $r = shift @tstr; - is($model->model_num, $r->[$i++]); - like($model->model_description, qr/$r->[$i++]/); - is($model->num_site_classes,$r->[$i++]); - my $tree = $model->next_tree; - is($model->kappa, $r->[$i++]); - is($model->likelihood,$r->[$i]); - is($tree->score, $r->[$i++]); - is($tree->total_branch_length, $r->[$i++]); - if( $iter == 0 ) { - my $params = $model->shape_params; - is($params->{'shape'}, 'alpha'); - is($params->{'gamma'}, '0.50000'); - is($params->{'r'}->[0], '1.00000'); - is($params->{'f'}->[0], '1.00000'); - } elsif( $iter == 2 ) { - my $class = $model->dnds_site_classes; - is($class->{'p'}->[0], '0.38160'); - is($class->{'w'}->[1], '1.00000'); - } - $iter++; - $lastmodel = $model; -} - -my ($firstsite) = $lastmodel->get_pos_selected_sites; -is($firstsite->[0], 15); -is($firstsite->[1], 'L'); -is($firstsite->[2], 0.6588); - -# codeml NSSites parsing -# for M0 model - -my $codeml_m0 = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('M0.mlc')); -ok($codeml_m0); -my $result_m0 = $codeml_m0->next_result; -my ($nssite_m0,$nssite_m1) = $result_m0->get_NSSite_results; -is($nssite_m0->num_site_classes,1); -my $class_m0 = $nssite_m0->dnds_site_classes; -is($class_m0->{q/p/}->[0],q/1.00000/); -is($class_m0->{q/w/}->[0],0.09213); - -is($nssite_m0->model_num, "0"); -@trees= $nssite_m0->get_trees; -is (@trees , 1 ); -# model 0 -is($trees[0]->score, -30.819156); -is($nssite_m1->model_num, "1"); -@trees= $nssite_m1->get_trees; -is($trees[0]->score, -30.819157); - -# test BASEML -# pairwise first - -my $baseml_p = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('baseml.pairwise')); -ok($baseml_p); -my $baseml = $baseml_p->next_result; -my @b_seqs = $baseml->get_seqs; -is($b_seqs[0]->seq, 'GTAGAGTACTTT'); -is($b_seqs[1]->seq, 'GTAAGAGACGAT'); - -my @otus = map { $_->display_id } @b_seqs; -is(scalar @otus, 3); -my $ntfreq = $baseml->get_NTFreqs; -ok($ntfreq); -is($ntfreq->{$otus[0]}->{'A'}, '0.3333'); -is($ntfreq->{$otus[1]}->{'G'}, '0.2105'); -my $kappaM = $baseml->get_KappaMatrix; -ok($kappaM); -is($kappaM->get_entry($otus[1],$otus[0]), '0.3240'); -is($kappaM->get_entry($otus[0],$otus[1]), - $kappaM->get_entry($otus[1],$otus[0])); -is($kappaM->get_entry($otus[1],$otus[2]), '0.1343'); -my $alphaM = $baseml->get_AlphaMatrix; -ok($alphaM); -is($alphaM->get_entry($otus[1],$otus[0]), '9.3595'); -is($alphaM->get_entry($otus[0],$otus[1]), - $alphaM->get_entry($otus[1],$otus[0])); -is($alphaM->get_entry($otus[1],$otus[2]), '1.1101'); -is($alphaM->get_entry($otus[0],$otus[2]), '33.1197'); - -# codeml NSSites parsing -# for only 1 model - -my $codeml_single = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('singleNSsite.mlc')); -ok($codeml_single); -my $result_single = $codeml_single->next_result; -my ($nssite_single) = $result_single->get_NSSite_results; -is($nssite_single->num_site_classes,q/3/); -is($nssite_single->kappa, q/5.28487/); -is($nssite_single->likelihood,q/-30.819156/); - -is($baseml->get_stat('loglikelihood'),-110.532715); -is($baseml->get_stat('constant_sites'),46); -is($baseml->get_stat('constant_sites_percentage'),'80.70'); -is($baseml->model,'HKY85 dGamma (ncatG=5)'); - -# user trees -$baseml_p = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('baseml.usertree')); -$baseml = $baseml_p->next_result; - -@trees = $baseml->get_trees; -is(@trees, 1); -is($trees[0]->score, -129.328757); - -# codeml NSSites parsing -# for branch site model/clade model - -my $codeml_bs = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('branchSite.mlc')); -ok($codeml_bs); -my $result_bs = $codeml_bs->next_result; -my ($nssite_bs) = $result_bs->get_NSSite_results; -is($nssite_bs->num_site_classes,q/4/); -my $class_bs = $nssite_bs->dnds_site_classes; -is($class_bs->{q/p/}->[1],q/0.65968/); -is($class_bs->{q/w/}->[1]->{q/background/},q/0.00000/); -is($class_bs->{q/w/}->[2]->{q/foreground/},q/999.00000/); - -# Let's parse the RST file - -my $paml = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml_lysozyme', 'mlc'), - -dir => test_input_file('codeml_lysozyme')); - -$result = $paml->next_result; - -my ($rst) = grep {$_->id eq 'node#8'} $result->get_rst_seqs; -ok($rst); -is($rst->seq, join('',qw( -AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGACTGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGATTATAACACA -CGAGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCACTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC -TGCAATGCTTTGCTGCAAGATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC -CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCATTGTCAAAACAGAGAT -GTCAGTCAGTATGTTCAAGGTTGTGGAGTG)), - 'node#8 reconstructed seq'); - -my ($first_tree) = $result->get_rst_trees; -my ($node) = $first_tree->find_node(-id => '5_Mmu_rhesus'); -my @changes = $node->get_tag_values('changes'); -my ($site) = grep { $_->{'site'} == 94 } @changes; -is($site->{'anc_aa'}, 'A','ancestral AA'); -is($site->{'anc_prob'}, '0.947','ancestral AA'); -is($site->{'derived_aa'}, 'T','derived AA'); - -($node) = $first_tree->find_node(-id => '12'); -@changes = $node->get_tag_values('changes'); -($site) = grep { $_->{'site'} == 88 } @changes; -is($site->{'anc_aa'}, 'N','ancestral AA'); -is($site->{'anc_prob'}, '0.993','ancestral AA'); -is($site->{'derived_aa'}, 'D','derived AA'); -is($site->{'derived_prob'}, '0.998','derived AA'); - -my $persite = $result->get_rst_persite; -# minus 1 because we have shifted so that array index matches site number -# there are 130 sites in this seq file -is(scalar @$persite -1, $result->patterns->{'-ls'}); -# let's score site 1 -$site = $persite->[2]; -# so site 2, node 2 (extant) -is($site->[2]->{'codon'}, 'GTC'); -is($site->[2]->{'aa'}, 'V'); -# site 2, node 3 -is($site->[3]->{'codon'}, 'ATC'); -is($site->[3]->{'aa'}, 'I'); - -# ancestral node 9 -is($site->[9]->{'codon'}, 'GTC'); -is($site->[9]->{'aa'}, 'V'); -is($site->[9]->{'prob'}, '1.000'); -is($site->[9]->{'Yang95_aa'},'V'); -is($site->[9]->{'Yang95_aa_prob'},'1.000'); - -# ancestral node 10 -is($site->[10]->{'codon'}, 'ATC'); -is($site->[10]->{'aa'}, 'I'); -is($site->[10]->{'prob'}, '0.992'); -is($site->[10]->{'Yang95_aa'},'I'); -is($site->[10]->{'Yang95_aa_prob'},'0.992'); - - -## PAML 3.15 -my $paml315 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml315.mlc')); -$result = $paml315->next_result; - -is($result->model, 'One dN/dS ratio'); -like($result->version, qr'3\.15'); -$MLmat = $result->get_MLmatrix; -$NGmat = $result->get_NGmatrix; - -is($NGmat->[0]->[1]->{'omega'}, 0.2264); -is($NGmat->[0]->[1]->{'dN'}, 0.0186); -is($NGmat->[0]->[1]->{'dS'}, 0.0821); - -is($MLmat->[0]->[1]->{'omega'}, 0.32693); -is($MLmat->[0]->[1]->{'dN'}, '0.0210'); -is($MLmat->[0]->[1]->{'dS'}, 0.0644); - -## PAML 4 -my $codeml4 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml4.mlc')); -$result = $codeml4->next_result; - -is($result->model, 'One dN/dS ratio'); -like($result->version, qr'4'); -$MLmat = $result->get_MLmatrix; -$NGmat = $result->get_NGmatrix; - -is($NGmat->[0]->[1]->{'omega'}, 0.2507); -is($NGmat->[0]->[1]->{'dN'}, 0.0863); -is($NGmat->[0]->[1]->{'dS'}, 0.3443); - -is($MLmat->[0]->[1]->{'omega'}, 0.29075); -is($MLmat->[0]->[1]->{'dN'}, '0.0874'); -is($MLmat->[0]->[1]->{'dS'}, 0.3006); -is($MLmat->[0]->[1]->{'lnL'}, -1596.739984); - -## PAML 4.3a -# codeml pairwise ML comparison (runmode=-2) -my $codeml43 = Bio::Tools::Phylo::PAML->new(-file => test_input_file('codeml43.mlc')); -$result = $codeml43->next_result; - -is($result->model, 'One dN/dS ratio for branches'); -like($result->version, qr'4\.3', 'codeml 4.3 runmode=-2'); -$MLmat = $result->get_MLmatrix; -$NGmat = $result->get_NGmatrix; - -is($NGmat->[0]->[2]->{'omega'}, 0.2627); -is($NGmat->[0]->[2]->{'dN'}, 0.0867); -is($NGmat->[0]->[2]->{'dS'}, 0.3301); - -is($MLmat->[0]->[2]->{'omega'}, 0.19819); -is($MLmat->[0]->[2]->{'dN'}, '0.0842'); -is($MLmat->[0]->[2]->{'dS'}, 0.4247); -is($MLmat->[0]->[2]->{'lnL'}, -1512.583367); - -## PAML 4.3a -# codeml NSSites parsing (two NSSites models, 1 and 2) -{ - my $codeml43_nssites = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml43_nssites.mlc')); - ok($codeml43_nssites); - - my $result = $codeml43_nssites->next_result; - ok($result); - - is($result->model, 'One dN/dS ratio for branches'); - like($result->version, qr'4\.3', 'codeml 4.3 two NSSites models'); - my $NGmat = $result->get_NGmatrix; - ok($NGmat); - - is($NGmat->[0]->[1]->{'omega'}, 0.2507); - is($NGmat->[0]->[1]->{'dN'}, 0.0863); - is($NGmat->[0]->[1]->{'dS'}, 0.3443); - is($NGmat->[1]->[2]->{'omega'}, 0.2943); - is($NGmat->[1]->[2]->{'dN'}, 0.1054); - is($NGmat->[1]->[2]->{'dS'}, 0.3581); - - # these are - # "model num" description "number of site classes" kappa log-likelihood "tree length" "time used" - my @tstr = ([qw(1 NearlyNeutral 2 2.06684 -2970.527521 2.898 0:08)], - [qw(2 PositiveSelection 3 2.18136 -2965.809712 3.589 0:26)],); - my $iter = 0; - my $lastmodel; - foreach my $model ( $result->get_NSSite_results ) { - my $i = 0; - my $r = shift @tstr; - is($model->model_num, $r->[$i++]); - like($model->model_description, qr/$r->[$i++]/); - is($model->num_site_classes,$r->[$i++]); - my $tree = $model->next_tree; - is($model->kappa, $r->[$i++]); - is($model->likelihood,$r->[$i]); - is($tree->score, $r->[$i++]); - like($tree->total_branch_length, qr/$r->[$i++]/); - if( $iter == 1 ) { - my $class = $model->dnds_site_classes; - is($class->{'p'}->[0], '0.83347'); - is($class->{'w'}->[1], '1.00000'); - } - $iter++; - $lastmodel = $model; - } - - my @sites = $lastmodel->get_NEB_pos_selected_sites; - my $firstsite = $sites[0]; - my $lastsite = $sites[-1]; - is($firstsite->[0], 35, 'NEB positively selected sites'); - is($firstsite->[1], 'S'); - is($firstsite->[2], 0.643); - is($firstsite->[4], '4.400'); - is( $lastsite->[0], 264); - is( $lastsite->[1], 'P'); - is( $lastsite->[2], 0.971); - is( $lastsite->[3], '*'); - is( $lastsite->[4], 6.134); -} - -# bug #3040 -{ - my $parser = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml_nan.mlc')); - ok($parser); - - my $result = $parser->next_result; - ok($result); - - my $MLmatrix = $result->get_MLmatrix(); - ok($MLmatrix); - - is($MLmatrix->[1]->[2]->{'dS'}, 'nan', 'bug 3040'); -} - -# bugs 3365, 3366 -{ - my $parser = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml45.mlc')); - - my $result = $parser->next_result; - - my @otus = $result->get_seqs(); - is(scalar @otus, 9, 'bug 3365'); - - my $MLmatrix = $result->get_MLmatrix(); - is($MLmatrix->[1]->[2]->{dN},0.0103,'bug 3366'); -} - -# bug 3367 -{ - my $parser = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('yn00_45.mlc')); - - my $result = $parser->next_result; - - my @otus = $result->get_seqs(); - is(scalar @otus, 9, 'bug 3367'); -} - -# bug 3332 -{ - my $parser = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('codeml45b.mlc')); - - my $result = $parser->next_result; - my $omega2 = $result->get_NGmatrix()->[0]->[1]->{'omega'}; - is($result->get_NGmatrix()->[0]->[1]->{'omega'}, '-1.0300', 'bug 3332'); -} - -# bug 3331 -{ - my $parser = Bio::Tools::Phylo::PAML->new - (-file => test_input_file('bug3331.mlc')); - my $result = $parser->next_result; - my $MLmatrix = $result->get_MLmatrix(); - my $kappa = $MLmatrix->[0]->[1]->{'kappa'}; - is ($kappa, '2.000', 'bug 3331'); -} diff --git a/t/data/M0.mlc b/t/data/M0.mlc deleted file mode 100644 index 2594bf149..000000000 --- a/t/data/M0.mlc +++ /dev/null @@ -1,159 +0,0 @@ -CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio -Codon frequencies: F3x4 -Site-class models: -ns = 3 ls = 6 - -Codon usage in sequences --------------------------------------------------------------------------- -Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 - TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 -Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 - TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 --------------------------------------------------------------------------- -Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 - CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 - CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 - CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 --------------------------------------------------------------------------- -Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 - ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 - ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 -Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 --------------------------------------------------------------------------- -Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 - GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 - GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 - GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 --------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: test0 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#2: test1 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#3: test2 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 - TTC 0 | TCC 1 | TAC 0 | TGC 0 -Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 - CTC 0 | CCC 1 | CAC 0 | CGC 0 - CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 - CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 - ATC 0 | ACC 0 | AAC 0 | AGC 0 - ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 -Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 - GTC 0 | GCC 0 | GAC 0 | GGC 0 - GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 - GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 -position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -test0 -test1 -1.0000 (0.0706 0.0000) -test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) - - -Model 0: one-ratio - - -TREE # 1: (1, 2, 3); MP score: 3 -lnL(ntime: 3 np: 5): -30.819156 +0.000000 - 4..1 4..2 4..3 - 0.25573 0.00000 0.62424 5.28487 0.09213 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.87997 - -(1: 0.255727, 2: 0.000004, 3: 0.624239); - -(test0: 0.255727, test1: 0.000004, test2: 0.624239); - -Detailed output identifying parameters - -kappa (ts/tv) = 5.28487 - -omega (dN/dS) = 0.09213 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 - 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 - 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 - -tree length for dN: 0.07702 -tree length for dS: 0.83594 - - -Time used: 0:00 - - -Model 1: NearlyNeutral (2 categories) - - -TREE # 1: (1, 2, 3); MP score: 3 -lnL(ntime: 3 np: 6): -30.819157 +0.000000 - 4..1 4..2 4..3 - 0.25573 0.00000 0.62424 5.28488 1.00000 0.09213 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.87997 - -(1: 0.255727, 2: 0.000004, 3: 0.624240); - -(test0: 0.255727, test1: 0.000004, test2: 0.624240); - -Detailed output identifying parameters - -kappa (ts/tv) = 5.28488 - - -dN/dS for site classes (K=2) - -p: 1.00000 0.00000 -w: 0.09213 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 - 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 - 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 - - -Naive Empirical Bayes (NEB) analysis -Time used: 0:02 diff --git a/t/data/aaml.mlc b/t/data/aaml.mlc deleted file mode 100644 index b7125ffaf..000000000 --- a/t/data/aaml.mlc +++ /dev/null @@ -1,54 +0,0 @@ -AAML (in paml 3.12 February 2002) stewart.aa Model: Empirical (wag.dat) -ns = 6 ls = 130 -# site patterns = 98 - 4 1 1 1 1 8 2 1 6 1 1 3 1 1 1 - 1 1 4 2 1 1 3 1 4 1 1 1 1 1 1 - 3 1 1 1 1 1 1 1 1 1 1 2 2 2 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 - -Langur KIFERCELAR TLKLGLDGYK VSNWVLAKWG NTETYNPGDE TDYIFQSRYN NGTPGAVDAH ISSALQNNIA DAVARVVSDP QIRVRNHQNK VSQVKGGV -Baboon .......... ..R......R I........D ..Q......Q .......H.. D......N.. ..N...D..T .......... .........R ....Q... -Human .V........ ..R..M...R I...M..... ..R...A..R .......... D......N.. L.....D... .......R.. ......R..R .R..Q... -Rat .TY....F.. ..RN.MS..Y ..D....QHN ..QR.D...Q .......... D...R.KN.G .P....DD.T Q.IQ...R.. ....QR.K.R L.GIRN.. -Cow .V........ .......... ....L.T..S ..K....SS. .......KW. D...N...G. V..EME.D.. K...KI..E- ..T.KS.RDH ..S.E.TL -Horse .V.SK....H K.AQEM..FG Y....M.EYN ..RFGKNANG S..L..NKWK DN-RSSSN.N .M.K.DE..D .DIS...R.. KMSKVK.KD. L.ELASNL - - - - -Frequencies.. - A R N D C Q E G H I L K M F P S T W Y V -Langur 0.1000 0.0462 0.0846 0.0538 0.0615 0.0385 0.0385 0.0846 0.0154 0.0462 0.0615 0.0692 0.0000 0.0154 0.0231 0.0615 0.0385 0.0385 0.0462 0.0769 -Baboon 0.0923 0.0615 0.0846 0.0692 0.0615 0.0615 0.0231 0.0769 0.0231 0.0538 0.0615 0.0385 0.0000 0.0154 0.0231 0.0538 0.0462 0.0385 0.0462 0.0692 -Human 0.1077 0.1077 0.0769 0.0615 0.0615 0.0462 0.0231 0.0846 0.0077 0.0385 0.0615 0.0385 0.0154 0.0154 0.0154 0.0462 0.0385 0.0385 0.0462 0.0692 -Rat 0.0846 0.0923 0.0692 0.0692 0.0615 0.0692 0.0231 0.0769 0.0154 0.0538 0.0462 0.0462 0.0077 0.0154 0.0308 0.0538 0.0462 0.0308 0.0615 0.0462 -Cow 0.0775 0.0233 0.0620 0.0543 0.0620 0.0155 0.0620 0.0620 0.0233 0.0388 0.0698 0.0930 0.0078 0.0155 0.0155 0.1008 0.0620 0.0465 0.0388 0.0698 -Horse 0.0853 0.0310 0.1008 0.0775 0.0620 0.0155 0.0465 0.0543 0.0155 0.0233 0.0775 0.1163 0.0310 0.0388 0.0078 0.1008 0.0078 0.0388 0.0310 0.0388 - -Average 0.0913 0.0604 0.0797 0.0643 0.0617 0.0411 0.0360 0.0733 0.0167 0.0424 0.0630 0.0668 0.0103 0.0193 0.0193 0.0694 0.0398 0.0386 0.0450 0.0617 -(Ambiguity characters are used to calculate freqs.) - - -# constant sites: 46 (35.38%) -AA distances (raw proportions of different sites) - -Langur -Baboon 0.1077 -Human 0.1385 0.1077 -Rat 0.2923 0.2538 0.2846 -Cow 0.2462 0.3000 0.3154 0.4231 -Horse 0.5000 0.5000 0.4923 0.4923 0.5462 - -TREE # 1: (((1, 2), 3), 4, (5, 6)); MP score: -1 -lnL(ntime: 9 np: 9): -1042.768973 +0.000000 - 7..8 8..9 9..1 9..2 8..3 7..4 7..10 10..5 10..6 - 0.00950 0.02220 0.08009 0.03337 0.06233 0.27133 0.09393 0.24105 0.58792 - -tree length = 1.40172 - -(((1:0.080088, 2:0.033370):0.022202, 3:0.062325):0.009497, 4:0.271333, (5:0.241055, 6:0.587920):0.093926); - -(((Langur:0.080088, Baboon:0.033370):0.022202, Human:0.062325):0.009497, Rat:0.271333, (Cow:0.241055, Horse:0.587920):0.093926); diff --git a/t/data/aaml_pairwise.mlc b/t/data/aaml_pairwise.mlc deleted file mode 100644 index 24da0ec4b..000000000 --- a/t/data/aaml_pairwise.mlc +++ /dev/null @@ -1,49 +0,0 @@ -AAML (in paml 3.13, August 2002) abglobin.aa Model: Empirical_F (wag.dat) -ns = 5 ls = 285 -# site patterns = 126 - 16 21 10 1 1 10 17 1 1 2 1 1 3 1 13 - 1 2 1 1 5 2 1 5 15 1 1 5 1 10 1 - 1 7 10 1 14 1 1 1 1 1 3 1 2 1 1 - 1 1 1 1 1 1 1 1 1 1 1 4 1 4 1 - 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 - -human VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK -goat-cow ...A...S.. .....GN.A. .......... .......... ....E.A.K. GL.LGT.D.. S.C..ND... .N..A.A... .F.K...... ..A...N..D S.NMKD.A.K ..V..R..VL .DF..R -rabbit .........I T..E.S.G.. ....V..... G.....FT.E .I.A.SE.K. GL.LG..T.. ..NH.S.... .N.SS..... .....E.... .SAN..N..A ..E.S..K.. ..I.S...Q. ...... -rat ...AD....I NC...G.G.. .E...Q...A A..S.IV.P. ...A...AKA D.ELG..T.F ..CH.GD..M ....DAA..N ....P.D..Y DSASI...IN .N..K..H.. MII.G.L.CA ..F.S. -marsupial ...D....H. .I...G..A. A....A.T.. ........P. .IQ....SQ. .L.LGTMK.. .I..SKDLE. F.A.S.NCI. TISQ..QTT. GS.G..SA.T SGEVK.YK.K IIIC.E.DEC V.WLH. - - - - -Frequencies.. - A R N D C Q E G H I L K M F P S T W Y V -human 0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053 -goat-cow 0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053 -rabbit 0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947 -rat 0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807 -marsupial 0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842 - -Average 0.1144 0.0211 0.0358 0.0554 0.0119 0.0182 0.0414 0.0730 0.0625 0.0133 0.1200 0.0828 0.0119 0.0533 0.0393 0.0646 0.0554 0.0112 0.0204 0.0940 - -# constant sites: 170 (59.65%) -ln Lmax (unconstrained) = -1189.106658 - -AA distances (raw proportions of different sites) - -human -goat-cow 0.1439 -rabbit 0.1368 0.1825 -rat 0.2000 0.2351 0.2035 -marsupial 0.2456 0.2561 0.2877 0.3123 - -ML distances of aa seqs. -human -goat-cow 0.1551 -rabbit 0.1474 0.2020 -rat 0.2267 0.2694 0.2306 -marsupial 0.2870 0.3024 0.3392 0.3861 diff --git a/t/data/baseml.pairwise b/t/data/baseml.pairwise deleted file mode 100644 index d34452407..000000000 --- a/t/data/baseml.pairwise +++ /dev/null @@ -1,31 +0,0 @@ - -seed used = 30455833 -BASEML (in paml 3.14, January 2004) m.phy HKY85 dGamma (ncatG=5) -ns = 3 ls = 57 -# site patterns = 12 - 7 16 15 1 3 2 1 1 8 1 1 1 - -wih99_snap GTAGAGTACT TT -wm276_snap ...AGAG..G A. -jec21_snap ....GACT.. CC - - - - -Frequencies.. - T C A G -wih99_snap 0.3509 0.1404 0.3333 0.1754 -wm276_snap 0.2982 0.1404 0.3509 0.2105 -jec21_snap 0.3158 0.1930 0.2982 0.1930 - -Average 0.3216 0.1579 0.3275 0.1930 - -# constant sites: 46 (80.70%) -ln Lmax (unconstrained) = -110.532715 - -Distances:HKY85 (kappa) (alpha set at 0.50) -This matrix is not used in later m.l. analysis. - -wih99_snap -wm276_snap 0.3240( 9.3595) -jec21_snap 0.2974(33.1197) 0.1343( 1.1101) diff --git a/t/data/baseml.usertree b/t/data/baseml.usertree deleted file mode 100644 index 604666313..000000000 --- a/t/data/baseml.usertree +++ /dev/null @@ -1,42 +0,0 @@ - -seed used = 30455833 -BASEML (in paml 3.14, January 2004) m.phy HKY85 dGamma (ncatG=5) -ns = 3 ls = 57 -# site patterns = 12 - 7 16 15 1 3 2 1 1 8 1 1 1 - -wih99_snap GTAGAGTACT TT -wm276_snap ...AGAG..G A. -jec21_snap ....GACT.. CC - - - - -Frequencies.. - T C A G -wih99_snap 0.3509 0.1404 0.3333 0.1754 -wm276_snap 0.2982 0.1404 0.3509 0.2105 -jec21_snap 0.3158 0.1930 0.2982 0.1930 - -Average 0.3216 0.1579 0.3275 0.1930 - -# constant sites: 46 (80.70%) -ln Lmax (unconstrained) = -110.532715 - -Distances:HKY85 (kappa) (alpha set at 0.50) -This matrix is not used in later m.l. analysis. - -wih99_snap -wm276_snap 0.3240( 9.3595) -jec21_snap 0.2974(33.1197) 0.1343( 1.1101) - -TREE # 1: (2, 3, 1); MP score: 13.00 -lnL(ntime: 3 np: 3): -129.328757 +0.000000 - 4..2 4..3 4..1 - 0.08669 0.05274 0.15105 - -tree length = 0.29048 - -(wm276_snap, jec21_snap, wih99_snap); - -(wm276_snap: 0.086692, jec21_snap: 0.052740, wih99_snap: 0.151050); diff --git a/t/data/branchSite.mlc b/t/data/branchSite.mlc deleted file mode 100644 index db8b2ed1a..000000000 --- a/t/data/branchSite.mlc +++ /dev/null @@ -1,115 +0,0 @@ -CODONML (in paml 3.15, November 2005) test.phy Model: several dN/dS ratios for branches -Codon frequencies: F3x4 -Site-class models: discrete (4 categories) -ns = 3 ls = 6 - -Codon usage in sequences --------------------------------------------------------------------------- -Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 - TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 -Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 - TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 --------------------------------------------------------------------------- -Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 - CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 - CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 - CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 --------------------------------------------------------------------------- -Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 - ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 - ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 -Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 --------------------------------------------------------------------------- -Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 - GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 - GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 - GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 --------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: test0 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#2: test1 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#3: test2 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 - TTC 0 | TCC 1 | TAC 0 | TGC 0 -Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 - CTC 0 | CCC 1 | CAC 0 | CGC 0 - CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 - CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 - ATC 0 | ACC 0 | AAC 0 | AGC 0 - ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 -Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 - GTC 0 | GCC 0 | GAC 0 | GGC 0 - GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 - GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 -position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -test0 -test1 -1.0000 (0.0706 0.0000) -test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) - - -TREE # 1: (1, 2, 3); MP score: 3 -lnL(ntime: 3 np: 9): -28.298935 +0.000000 - 4..1 4..2 4..3 - 0.31500 0.00000 18.45220 99.00000 0.00000 0.65968 0.00000 0.00000 999.00000 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 18.76720 - -(1: 0.314996, 2: 0.000004, 3: 18.452204); - -(test0: 0.314996, test1: 0.000004, test2: 18.452204); - -Detailed output identifying parameters - -kappa (ts/tv) = 99.00000 - - -dN/dS for site classes (K=4) - -site class 0 1 2a 2b -proportion 0.00000 0.65968 0.00000 0.34032 -background w 0.00000 0.00000 0.00000 0.00000 -foreground w 0.00000 0.00000999.00000 999.00000 - - -Naive Empirical Bayes (NEB) analysis (please use the BEB results.) -Positive sites for foreground lineages Prob(w>1): - - 2 M 1.000** diff --git a/t/data/bug3331.mlc b/t/data/bug3331.mlc deleted file mode 100644 index 6b4edfc92..000000000 --- a/t/data/bug3331.mlc +++ /dev/null @@ -1,128 +0,0 @@ - 2 195 - -seq1 GTT ACC GGT CTT GAC ATG AAC ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTT TTA GGT -seq2 GTT GCT GGT CTT GAC ATG AAT ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTC TTA GGT - - - -Printing out site pattern counts - - - 2 111 P - -seq1 AAA AAC AAT ACA ACC AGA AGC ATA ATC ATG ATT CAA CAC CAG CAT CGC CGG CTA CTT CTT GAA GAC GAG GAT GCA GCT GGA GGC GGG GGT GTA GTG GTT TAT TTA TTG TTT -seq2 ... ..T ... ... G.T ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... - - 4 1 1 2 1 1 2 1 4 2 1 1 3 1 1 - 1 1 2 1 4 6 1 1 3 1 1 1 2 1 3 - 1 1 1 1 2 2 2 - -CODONML (in paml version 4.5, December 2011) /var/folders/pr/wb88nxq93xn7hdhgr2_bjd5w0000gn/T/UIa4SSyGGv/Bw_1hNQpYZ -Model: One dN/dS ratio for branches kappa = 2.000 fixed - -Codon frequency model: F3x4 -ns = 2 ls = 65 - -Codon usage in sequences --------------------------------------------------------------- -Phe TTT 2 2 | Ser TCT 0 0 | Tyr TAT 1 1 | Cys TGT 0 0 - TTC 0 0 | TCC 0 0 | TAC 0 0 | TGC 0 0 -Leu TTA 2 2 | TCA 0 0 | *** TAA 0 0 | *** TGA 0 0 - TTG 2 2 | TCG 0 0 | TAG 0 0 | Trp TGG 0 0 --------------------------------------------------------------- -Leu CTT 5 4 | Pro CCT 0 0 | His CAT 1 1 | Arg CGT 0 0 - CTC 0 1 | CCC 0 0 | CAC 3 3 | CGC 1 1 - CTA 2 2 | CCA 0 0 | Gln CAA 1 1 | CGA 0 0 - CTG 0 0 | CCG 0 0 | CAG 1 1 | CGG 1 1 --------------------------------------------------------------- -Ile ATT 1 1 | Thr ACT 0 0 | Asn AAT 1 2 | Ser AGT 0 0 - ATC 4 4 | ACC 1 0 | AAC 1 0 | AGC 2 2 - ATA 1 1 | ACA 2 2 | Lys AAA 4 4 | Arg AGA 1 1 -Met ATG 2 2 | ACG 0 0 | AAG 0 0 | AGG 0 0 --------------------------------------------------------------- -Val GTT 1 1 | Ala GCT 1 2 | Asp GAT 3 3 | Gly GGT 3 3 - GTC 0 0 | GCC 0 0 | GAC 1 1 | GGC 2 2 - GTA 1 1 | GCA 1 1 | Glu GAA 6 6 | GGA 1 1 - GTG 1 1 | GCG 0 0 | GAG 1 1 | GGG 1 1 --------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: seq1 -position 1: T:0.10769 C:0.23077 A:0.30769 G:0.35385 -position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 -position 3: T:0.29231 C:0.23077 A:0.33846 G:0.13846 -Average T:0.25641 C:0.17949 A:0.33846 G:0.22564 - -#2: seq2 -position 1: T:0.10769 C:0.23077 A:0.29231 G:0.36923 -position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 -position 3: T:0.30769 C:0.21538 A:0.33846 G:0.13846 -Average T:0.26154 C:0.17436 A:0.33333 G:0.23077 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 4 | Ser S TCT 0 | Tyr Y TAT 2 | Cys C TGT 0 - TTC 0 | TCC 0 | TAC 0 | TGC 0 -Leu L TTA 4 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 4 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 9 | Pro P CCT 0 | His H CAT 2 | Arg R CGT 0 - CTC 1 | CCC 0 | CAC 6 | CGC 2 - CTA 4 | CCA 0 | Gln Q CAA 2 | CGA 0 - CTG 0 | CCG 0 | CAG 2 | CGG 2 ------------------------------------------------------------------------------- -Ile I ATT 2 | Thr T ACT 0 | Asn N AAT 3 | Ser S AGT 0 - ATC 8 | ACC 1 | AAC 1 | AGC 4 - ATA 2 | ACA 4 | Lys K AAA 8 | Arg R AGA 2 -Met M ATG 4 | ACG 0 | AAG 0 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 2 | Ala A GCT 3 | Asp D GAT 6 | Gly G GGT 6 - GTC 0 | GCC 0 | GAC 2 | GGC 4 - GTA 2 | GCA 2 | Glu E GAA 12 | GGA 2 - GTG 2 | GCG 0 | GAG 2 | GGG 2 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.10769 C:0.23077 A:0.30000 G:0.36154 -position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462 -position 3: T:0.30000 C:0.22308 A:0.33846 G:0.13846 -Average T:0.25897 C:0.17692 A:0.33590 G:0.22821 - -Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): - 0.01224357 0.00910419 0.01381326 0.00565088 - 0.00255074 0.00189671 0.00287776 0.00117727 - 0.01224357 0.00910419 0.00000000 0.00000000 - 0.00612179 0.00455210 0.00000000 0.00282544 - 0.02623622 0.01950899 0.02959984 0.01210903 - 0.00546588 0.00406437 0.00616663 0.00252271 - 0.02623622 0.01950899 0.02959984 0.01210903 - 0.01311811 0.00975449 0.01479992 0.00605451 - 0.03410709 0.02536168 0.03847979 0.01574173 - 0.00710564 0.00528368 0.00801662 0.00327953 - 0.03410709 0.02536168 0.03847979 0.01574173 - 0.01705355 0.01268084 0.01923990 0.00787087 - 0.04110342 0.03056408 0.04637309 0.01897081 - 0.00856321 0.00636752 0.00966106 0.00395225 - 0.04110342 0.03056408 0.04637309 0.01897081 - 0.02055171 0.01528204 0.02318654 0.00948540 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later ML. analysis. -Use runmode = -2 for ML pairwise comparison.) - -seq1 -seq2 0.0913 (0.0066 0.0726) - -pairwise comparison, codon frequencies: F3x4. - - -2 (seq2) ... 1 (seq1) -lnL = -272.706911 - 0.06846 0.10294 - -t= 0.0685 S= 51.9 N= 143.1 dN/dS= 0.1029 dN = 0.0069 dS = 0.0668 diff --git a/t/data/codeml.mlc b/t/data/codeml.mlc deleted file mode 100644 index 815319930..000000000 --- a/t/data/codeml.mlc +++ /dev/null @@ -1,190 +0,0 @@ -CODONML (in paml 3.12 February 2002) abglobin.nuc Model: several dN/dS ratios for branches -Codon frequencies: F3x4 - -ns = 5 ls = 285 -# site patterns = 223 - 9 2 1 1 1 4 3 1 1 1 2 1 1 3 1 - 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 5 1 1 1 4 2 2 1 6 1 1 1 1 - 1 3 1 1 3 1 1 1 2 3 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 - 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 - 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 - 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 - 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 - -1 -human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC CCC ACC ACC TAC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG GTG GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC CTG CAC GCG CTT CGG GAC CCG GTC AAC TTC CTC CTA AGC TGC CTG CTG GCC GCC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GCT TCT AGC ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG TCT GCC GTT ACT GCC CTG GGC AAC GTG GAT GAA GTT GGT GGT CTG AGG CTG GTG GTC CCT ACC CAG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT GTG AAG GCT CAT AAG AAA CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG TTT GCC ACA CTG AGT GAG TGT CAC GAT CCT AAC AGG CTC GGC AAC GTG CTG GTC TGT GTG GCC CAT CAC TTT AAA GAA TTC ACC CCA CCA GTG GCT GCC TAT GTG GGT AAT GCC AAG TAT CAC -goat-cow ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... .C. ... ... ... ..A ..G ... .GC C.. ... C.. ... GGT A.T ... ..T .AT ... ..T ... ... ..C ..G ..T ... ... ... ... ..T ..T ..G ... .C. ... ... ... TG. ... ... AAT ..T ... ... ..C ... ..C ... ... ... T.. ..C AAC ... ... ... ... ... ... ... ... G.. ... ... G.. ... ..C ..C ... T.T ... ..A ... ... ... ... ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ... ..C T.. ... ... G.. ... ... ... ... AA. ... ... ... ... ..C ... ... ..G ..A .A. T.. ... ... A.. ... A.. AAG ..T ..C ..T G.. ... ... ... ..T G.G ... ... ... ... ..T ... ... ... .A. ... ... ... ... ..A ..G GT. ... ..T .GC A.T ... ..G ... ... ... ..G GTG C.. ... .A. .T. ... ... ... ... .GA ... ..T -rabbit ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... T.. ..A ..C ... ... ..G ... ... .GC C.. ... C.. ... GG. ..C ... ..T A.T ..C ... ... ... ... ..G ... ... ... ..G ..T ... ... ..G TC. ... ... ... ... AA. .A. ... AGT ..A ... ... ... ... ... ..T ... ... ... ..C AAC ... ... ... ... ..T ... ... T.C AG. ... ... ... ..G ..C ... ... ... ... ..T ... ..A ... ... ... ... ... ... ... ..T ... ..A ... ... ... ..C ... ... ... ... ..C ... ... T.. G.A A.. ... ... ... AA. ..T ... ... ... ... ... ... ..G ..G .C. ... ..C ... ..G ..T ... AG. ... ... ... ... ... ..A ... ..T .AG ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T AT. ... T.T ... ..T ... ... ... ... ..T ..T .AG ... ... ... ... ... ... ... ..T ..A ..C ... -rat ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ..T ..T ..C T.. G.. ..A ..T .CA .AC ..C ..A C.. ..T GGT ..C ... ... A.T ... ... ... ..T ..C ..G ..T ..T ..T ... ... ... T.. ..G ... ... ... T.. ..T TG. .A. ..T .GA ..T ... ..A ..C ..C A.. ... ... ..T ..T ..C ... ... ..T ... ..G ... ... ..A ... GA. .CT ... G.. ..T ... .A. ... ... ..A ... CCT ... ..T ... ... ..C ... ... ... ..T ... ... ... ... .A. ... ..T AG. ... ... ..C ... ... T.. G.C TC. ... A.C ... ..T ... ... ... ... ..C ... ... ..G A.A AAC ... ..C .A. ... ... ... AAA ... T.. ... ... ... ... ... ..T CAT ... ... ..A ... ..T ... ... ... ... ... ... ..T A.. A.T ..G AT. ... .G. ..C ... C.G ..G ... ... ... ..C TGT .CA ... ... .TC ... ..A .G. ..T ... ..C ... -marsupial ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... ..A ... ..T ..C ..T T.. C.G ..T ..T ..C C.. ... C.. ... GGA A.C A.. ... AAA ..A ... ... ... ..C ..G A.A ..T ..C ..G ... ... ... ..C TCT ... A.C ... ... ... ..G AG. AAG ..T ..G ..T ..C .AA ... ... ... ... T.T ..C ... GCT ... ..G ..G ... ... T.. ... T.. ... ... AAC TG. A.C ... A.. A.C TCT C.G ..T ..C C.G AC. ... ... ..T ... ..C ..T ... ..C ... ACC ..T ... .G. AG. ... ..T ... ... ... T.. ... .GC ... ..C ... TCA ..T T.. ..T C.A ..C ... GCT ..G T.G ACC T.. ..C G.. ..A .CA G.C AAG ..T T.. ... ... ..G ... .A. ... .AG T.. ... ... ... ..T ..C ... ... .A. A.G ..G ..T A.C A.T ..G ATC TGC ..T G.G ... ... ..G ..T ..T ..T ..T GA. TGT .T. ..T .GG C.C ..A C.. ... ... ..C ... - -Codon usage in sequences --------------------------------------------------------------------------------------------------- -Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 - TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 --------------------------------------------------------------------------------------------------- -Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 - CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 - CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 - CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 - ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 - ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 -Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 --------------------------------------------------------------------------------------------------- -Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 - GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 - GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 - GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: human -position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 -position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 -position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 - -#2: goat-cow -position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 -position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 -position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 - -#3: rabbit -position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 -position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 -position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 - -#4: rat -position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 -position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 -position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 - -#5: marsupial -position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 -position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 -position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 - TTC 51 | TCC 31 | TAC 19 | TGC 9 -Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 - TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------- -Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 - CTC 24 | CCC 25 | CAC 68 | CGC 1 - CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 - CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------- -Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 - ATC 12 | ACC 53 | AAC 35 | AGC 19 - ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 -Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------- -Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 - GTC 19 | GCC 92 | GAC 48 | GGC 60 - GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 - GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 -position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 -position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -human -goat-cow 0.2507 (0.0863 0.3443) -rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) -rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) -marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) - -pairwise comparison, codon frequencies: F3x4. - - -2 (goat-cow) ... 1 (human) -lnL =-1508.607268 - 0.47825 2.29137 0.19479 - -t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309 - - -3 (rabbit) ... 1 (human) -lnL =-1512.583367 - 0.46755 2.19039 0.19819 - -t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247 - - -3 (rabbit) ... 2 (goat-cow) -lnL =-1557.337680 - 0.53837 2.26427 0.22670 - -t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570 - - -4 (rat) ... 1 (human) -lnL =-1649.727994 - 0.82576 1.78920 0.15108 - -t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097 - - -4 (rat) ... 2 (goat-cow) -lnL =-1677.101606 - 0.88091 2.40576 0.18757 - -t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773 - - -4 (rat) ... 3 (rabbit) -lnL =-1666.440696 - 0.85281 2.21652 0.16114 - -t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105 - - -5 (marsupial) ... 1 (human) -lnL =-1769.079306 - 2.29076 0.98664 0.05689 - -t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396 - - -5 (marsupial) ... 2 (goat-cow) -lnL =-1774.766235 - 1.80490 1.19637 0.08052 - -t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879 - - -5 (marsupial) ... 3 (rabbit) -lnL =-1794.595175 - 2.09985 1.06589 0.06930 - -t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162 - - -5 (marsupial) ... 4 (rat) -lnL =-1842.638722 - 1.66307 1.02118 0.12318 - -t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973 diff --git a/t/data/codeml315.mlc b/t/data/codeml315.mlc deleted file mode 100644 index 62a7593ff..000000000 --- a/t/data/codeml315.mlc +++ /dev/null @@ -1,132 +0,0 @@ -CODONML (in paml 3.15, November 2005) /tmp/I7ZhE4PgvE/V8dSv7iz0l Model: One dN/dS ratio -Codon frequencies: F3x4 -ns = 4 ls = 573 - -Codon usage in sequences --------------------------------------------------------------------------------------- -Phe TTT 4 4 5 3 | Ser TCT 16 15 11 15 | Tyr TAT 11 11 14 14 | Cys TGT 2 1 2 1 - TTC 7 7 8 8 | TCC 12 8 16 8 | TAC 14 14 10 11 | TGC 1 2 1 2 -Leu TTA 1 1 1 2 | TCA 5 7 3 6 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0 - TTG 5 5 8 7 | TCG 5 5 8 6 | TAG 0 0 0 0 | Trp TGG 6 6 6 6 --------------------------------------------------------------------------------------- -Leu CTT 7 7 10 8 | Pro CCT 22 21 18 17 | His CAT 5 3 3 5 | Arg CGT 3 2 2 2 - CTC 14 15 13 17 | CCC 11 13 12 16 | CAC 4 3 5 5 | CGC 4 5 5 4 - CTA 1 1 0 2 | CCA 12 13 14 11 | Gln CAA 38 38 40 38 | CGA 4 3 4 2 - CTG 7 7 4 4 | CCG 14 13 12 13 | CAG 33 34 28 31 | CGG 2 3 4 5 --------------------------------------------------------------------------------------- -Ile ATT 3 4 4 3 | Thr ACT 6 8 4 5 | Asn AAT 9 10 9 6 | Ser AGT 3 3 5 3 - ATC 11 11 9 10 | ACC 5 4 7 7 | AAC 14 13 12 15 | AGC 4 4 5 6 - ATA 1 2 2 2 | ACA 4 3 9 8 | Lys AAA 6 7 5 4 | Arg AGA 6 7 7 7 -Met ATG 9 9 11 8 | ACG 10 9 5 5 | AAG 16 15 17 19 | AGG 7 7 4 5 --------------------------------------------------------------------------------------- -Val GTT 3 4 5 5 | Ala GCT 16 16 16 18 | Asp GAT 14 14 15 18 | Gly GGT 17 16 17 18 - GTC 8 8 8 8 | GCC 19 18 15 18 | GAC 13 15 13 10 | GGC 8 9 10 9 - GTA 7 6 7 6 | GCA 16 17 11 14 | Glu GAA 16 17 19 15 | GGA 7 7 4 6 - GTG 5 7 6 7 | GCG 10 8 18 10 | GAG 24 22 21 23 | GGG 6 6 6 6 --------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: R265 -position 1: T:0.15532 C:0.31588 A:0.19895 G:0.32984 -position 2: T:0.16230 C:0.31937 A:0.37871 G:0.13962 -position 3: T:0.24607 C:0.26003 A:0.21640 G:0.27749 - -#2: WM276 -position 1: T:0.15009 C:0.31588 A:0.20244 G:0.33159 -position 2: T:0.17103 C:0.31065 A:0.37696 G:0.14136 -position 3: T:0.24258 C:0.26003 A:0.22513 G:0.27225 - -#3: H99 -position 1: T:0.16230 C:0.30366 A:0.20070 G:0.33333 -position 2: T:0.17627 C:0.31239 A:0.36824 G:0.14311 -position 3: T:0.24433 C:0.26003 A:0.21990 G:0.27574 - -#4: JEC21 -position 1: T:0.15532 C:0.31414 A:0.19721 G:0.33333 -position 2: T:0.17452 C:0.30890 A:0.37347 G:0.14311 -position 3: T:0.24607 C:0.26876 A:0.21466 G:0.27051 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 16 | Ser S TCT 57 | Tyr Y TAT 50 | Cys C TGT 6 - TTC 30 | TCC 44 | TAC 49 | TGC 6 -Leu L TTA 5 | TCA 21 | *** * TAA 0 | *** * TGA 0 - TTG 25 | TCG 24 | TAG 0 | Trp W TGG 24 ------------------------------------------------------------------------------- -Leu L CTT 32 | Pro P CCT 78 | His H CAT 16 | Arg R CGT 9 - CTC 59 | CCC 52 | CAC 17 | CGC 18 - CTA 4 | CCA 50 | Gln Q CAA 154 | CGA 13 - CTG 22 | CCG 52 | CAG 126 | CGG 14 ------------------------------------------------------------------------------- -Ile I ATT 14 | Thr T ACT 23 | Asn N AAT 34 | Ser S AGT 14 - ATC 41 | ACC 23 | AAC 54 | AGC 19 - ATA 7 | ACA 24 | Lys K AAA 22 | Arg R AGA 27 -Met M ATG 37 | ACG 29 | AAG 67 | AGG 23 ------------------------------------------------------------------------------- -Val V GTT 17 | Ala A GCT 66 | Asp D GAT 61 | Gly G GGT 68 - GTC 32 | GCC 70 | GAC 51 | GGC 36 - GTA 26 | GCA 58 | Glu E GAA 67 | GGA 24 - GTG 25 | GCG 46 | GAG 90 | GGG 24 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.15576 C:0.31239 A:0.19983 G:0.33202 -position 2: T:0.17103 C:0.31283 A:0.37435 G:0.14180 -position 3: T:0.24476 C:0.26222 A:0.21902 G:0.27400 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -R265 -WM276 0.2264 (0.0186 0.0821) -H99 0.1481 (0.0586 0.3959) 0.1481 (0.0611 0.4126) -JEC21 0.1112 (0.0421 0.3787) 0.1173 (0.0466 0.3970) 0.1419 (0.0380 0.2679) - -pairwise comparison, codon frequencies: F3x4. - - -2 (WM276) ... 1 (R265) -lnL =-2569.912690 - 0.10404 3.29148 0.32693 - -t= 0.1040 S= 541.4 N= 1177.6 dN/dS= 0.3269 dN= 0.0210 dS= 0.0644 - - -3 (H99) ... 1 (R265) -lnL =-3019.970151 - 0.43604 3.31017 0.20554 - -t= 0.4360 S= 540.2 N= 1178.8 dN/dS= 0.2055 dN= 0.0656 dS= 0.3193 - - -3 (H99) ... 2 (WM276) -lnL =-3036.174074 - 0.45547 3.63495 0.20989 - -t= 0.4555 S= 547.4 N= 1171.6 dN/dS= 0.2099 dN= 0.0691 dS= 0.3290 - - -4 (JEC21) ... 1 (R265) -lnL =-2937.357570 - 0.38462 2.95077 0.15134 - -t= 0.3846 S= 530.2 N= 1188.8 dN/dS= 0.1513 dN= 0.0470 dS= 0.3104 - - -4 (JEC21) ... 2 (WM276) -lnL =-2966.384266 - 0.41002 3.25414 0.16413 - -t= 0.4100 S= 538.1 N= 1180.9 dN/dS= 0.1641 dN= 0.0527 dS= 0.3210 - - -4 (JEC21) ... 3 (H99) -lnL =-2844.283241 - 0.29120 4.67661 0.21504 - -t= 0.2912 S= 566.5 N= 1152.5 dN/dS= 0.2150 dN= 0.0441 dS= 0.2049 diff --git a/t/data/codeml4.mlc b/t/data/codeml4.mlc deleted file mode 100644 index 7cbdcdc3a..000000000 --- a/t/data/codeml4.mlc +++ /dev/null @@ -1,230 +0,0 @@ - -seed used = 480745521 - 5 855 - -human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC ACC ACC AAG ACC TAC TTC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG CAC GTG GAC GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC GAC CTG CAC GCG CAC AAG CTT CGG GTG GAC CCG GTC AAC TTC AAG CTC CTA AGC CAC TGC CTG CTG GTG ACC CTG GCC GCC CAC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GAC AAG TTC CTG GCT TCT GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT GCC CTG TGG GGC AAG GTG AAC GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTG GTC TAC CCT TGG ACC CAG AGG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT AAG GTG AAG GCT CAT GGC AAG AAA GTG CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG GGC ACC TTT GCC ACA CTG AGT GAG CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTC TGT GTG CTG GCC CAT CAC TTT GGC AAA GAA TTC ACC CCA CCA GTG CAG GCT GCC TAT CAG AAA GTG GTG GCT GGT GTG GCT AAT GCC CTG GCC CAC AAG TAT CAC -goat-cow GTG CTG TCT GCC GCC GAC AAG TCC AAT GTC AAG GCC GCC TGG GGC AAG GTT GGC GGC AAC GCT GGA GCT TAT GGC GCA GAG GCT CTG GAG AGG ATG TTC CTG AGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC CTG AGC CAC GGC TCG GCC CAG GTC AAG GGC CAC GGC GAG AAG GTG GCC GCC GCG CTG ACC AAA GCG GTG GGC CAC CTG GAC GAC CTG CCC GGT ACT CTG TCT GAT CTG AGT GAC CTG CAC GCC CAC AAG CTG CGT GTG GAC CCG GTC AAC TTT AAG CTT CTG AGC CAC TCC CTG CTG GTG ACC CTG GCC TGC CAC CTC CCC AAT GAT TTC ACC CCC GCG GTC CAC GCC TCC CTG GAC AAG TTC TTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT GCT GAG GAG AAG GCT GCC GTC ACC GCC TTT TGG GGC AAG GTG AAA GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCC TGG ACT CAG AGG TTC TTT GAG TCC TTT GGG GAC TTG TCC ACT GCT GAT GCT GTT ATG AAC AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG CTA GAT TCC TTT AGT AAT GGC ATG AAG CAT CTC GAT GAC CTC AAG GGC ACC TTT GCT GCG CTG AGT GAG CTG CAC TGT GAT AAG CTG CAT GTG GAT CCT GAG AAC TTC AAG CTC CTG GGC AAC GTG CTA GTG GTT GTG CTG GCT CGC AAT TTT GGC AAG GAA TTC ACC CCG GTG CTG CAG GCT GAC TTT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCC CAC AGA TAT CAT -rabbit GTG CTG TCT CCC GCT GAC AAG ACC AAC ATC AAG ACT GCC TGG GAA AAG ATC GGC AGC CAC GGT GGC GAG TAT GGC GCC GAG GCC GTG GAG AGG ATG TTC TTG GGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC TTC ACC CAC GGC TCT GAG CAG ATC AAA GCC CAC GGC AAG AAG GTG TCC GAA GCC CTG ACC AAG GCC GTG GGC CAC CTG GAC GAC CTG CCC GGC GCC CTG TCT ACT CTC AGC GAC CTG CAC GCG CAC AAG CTG CGG GTG GAC CCG GTG AAT TTC AAG CTC CTG TCC CAC TGC CTG CTG GTG ACC CTG GCC AAC CAC CAC CCC AGT GAA TTC ACC CCT GCG GTG CAT GCC TCC CTG GAC AAG TTC CTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAT CGT CTG TCC AGT GAG GAG AAG TCT GCG GTC ACT GCC CTG TGG GGC AAG GTG AAT GTG GAA GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCA TGG ACC CAG AGG TTC TTC GAG TCC TTT GGG GAC CTG TCC TCT GCA AAT GCT GTT ATG AAC AAT CCT AAG GTG AAG GCT CAT GGC AAG AAG GTG CTG GCT GCC TTC AGT GAG GGT CTG AGT CAC CTG GAC AAC CTC AAA GGC ACC TTT GCT AAG CTG AGT GAA CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTT ATT GTG CTG TCT CAT CAT TTT GGC AAA GAA TTC ACT CCT CAG GTG CAG GCT GCC TAT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCT CAC AAA TAC CAC -rat GTG CTC TCT GCA GAT GAC AAA ACC AAC ATC AAG AAC TGC TGG GGG AAG ATT GGT GGC CAT GGT GGT GAA TAT GGC GAG GAG GCC CTA CAG AGG ATG TTC GCT GCC TTC CCC ACC ACC AAG ACC TAC TTC TCT CAC ATT GAT GTA AGC CCC GGC TCT GCC CAG GTC AAG GCT CAC GGC AAG AAG GTT GCT GAT GCC TTG GCC AAA GCT GCA GAC CAC GTC GAA GAC CTG CCT GGT GCC CTG TCC ACT CTG AGC GAC CTG CAT GCC CAC AAA CTG CGT GTG GAT CCT GTC AAC TTC AAG TTC CTG AGC CAC TGC CTG CTG GTG ACC TTG GCT TGC CAC CAC CCT GGA GAT TTC ACA CCC GCC ATG CAC GCC TCT CTG GAC AAA TTC CTT GCC TCT GTG AGC ACT GTG CTG ACC TCC AAG TAC CGT CTA ACT GAT GCT GAG AAG GCT GCT GTT AAT GCC CTG TGG GGA AAG GTG AAC CCT GAT GAT GTT GGT GGC GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCT TGG ACC CAG AGG TAC TTT GAT AGC TTT GGG GAC CTG TCC TCT GCC TCT GCT ATC ATG GGT AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG ATA AAC GCC TTC AAT GAT GGC CTG AAA CAC TTG GAC AAC CTC AAG GGC ACC TTT GCT CAT CTG AGT GAA CTC CAC TGT GAC AAG CTG CAT GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAT ATG ATT GTG ATT GTG TTG GGC CAC CAC CTG GGC AAG GAA TTC ACC CCC TGT GCA CAG GCT GCC TTC CAG AAG GTG GTG GCT GGA GTG GCC AGT GCC CTG GCT CAC AAG TAC CAC -marsupial GTG CTC TCG GAT GCT GAC AAG ACT CAC GTG AAA GCC ATC TGG GGT AAG GTG GGA GGC CAC GCC GGT GCC TAC GCA GCT GAA GCT CTT GCC AGA ACC TTC CTC TCC TTC CCC ACT ACC AAA ACT TAC TTC CCC CAC TTC GAC CTG TCC CCC GGC TCC GCC CAG ATC CAG GGT CAT GGT AAG AAG GTA GCC GAT GCC CTT TCC CAG GCT GTT GCC CAC CTG GAC GAC CTG CCC GGA ACC ATG TCC AAA CTA AGC GAC CTG CAC GCC CAC AAG CTG AGA GTG GAT CCC GTG AAC TTC AAG CTC CTC TCT CAC TGC CTG ATC GTG ACT CTG GCC GCC CAT CTG AGC AAG GAT TTG ACT CCC GAA GTG CAC GCC TCC ATG GAC AAG TTC TTT GCC TCT GTG GCT ACC GTG CTG ACC TCG AAG TAC CGT TTG ACT TCT GAG GAG AAG AAC TGC ATC ACT ACC ATC TGG TCT AAG GTG CAG GTT GAC CAG ACT GGT GGT GAG GCC CTT GGC AGG ATG CTC GTT GTC TAC CCC TGG ACC ACC AGG TTT TTT GGG AGC TTT GGT GAT CTG TCC TCT CCT GGC GCT GTC ATG TCA AAT TCT AAG GTT CAA GCC CAT GGT GCT AAG GTG TTG ACC TCC TTC GGT GAA GCA GTC AAG CAT TTG GAC AAC CTG AAG GGT ACT TAT GCC AAG TTG AGT GAG CTC CAC TGT GAC AAG CTG CAT GTG GAC CCT GAG AAC TTC AAG ATG CTG GGG AAT ATC ATT GTG ATC TGC CTG GCT GAG CAC TTT GGC AAG GAT TTT ACT CCT GAA TGT CAG GTT GCT TGG CAG AAG CTC GTG GCT GGA GTT GCC CAT GCC CTG GCC CAC AAG TAC CAC - - - -Printing out site pattern counts - - - 5 669 P - -human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC CCC ACC ACC TAC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG GTG GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC CTG CAC GCG CTT CGG GAC CCG GTC AAC TTC CTC CTA AGC TGC CTG CTG GCC GCC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GCT TCT AGC ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG TCT GCC GTT ACT GCC CTG GGC AAC GTG GAT GAA GTT GGT GGT CTG AGG CTG GTG GTC CCT ACC CAG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT GTG AAG GCT CAT AAG AAA CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG TTT GCC ACA CTG AGT GAG TGT CAC GAT CCT AAC AGG CTC GGC AAC GTG CTG GTC TGT GTG GCC CAT CAC TTT AAA GAA TTC ACC CCA CCA GTG GCT GCC TAT GTG GGT AAT GCC AAG TAT CAC -goat-cow ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... .C. ... ... ... ..A ..G ... .GC C.. ... C.. ... GGT A.T ... ..T .AT ... ..T ... ... ..C ..G ..T ... ... ... ... ..T ..T ..G ... .C. ... ... ... TG. ... ... AAT ..T ... ... ..C ... ..C ... ... ... T.. ..C AAC ... ... ... ... ... ... ... ... G.. ... ... G.. ... ..C ..C ... T.T ... ..A ... ... ... ... ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ... ..C T.. ... ... G.. ... ... ... ... AA. ... ... ... ... ..C ... ... ..G ..A .A. T.. ... ... A.. ... A.. AAG ..T ..C ..T G.. ... ... ... ..T G.G ... ... ... ... ..T ... ... ... .A. ... ... ... ... ..A ..G GT. ... ..T .GC A.T ... ..G ... ... ... ..G GTG C.. ... .A. .T. ... ... ... ... .GA ... ..T -rabbit ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... T.. ..A ..C ... ... ..G ... ... .GC C.. ... C.. ... GG. ..C ... ..T A.T ..C ... ... ... ... ..G ... ... ... ..G ..T ... ... ..G TC. ... ... ... ... AA. .A. ... AGT ..A ... ... ... ... ... ..T ... ... ... ..C AAC ... ... ... ... ..T ... ... T.C AG. ... ... ... ..G ..C ... ... ... ... ..T ... ..A ... ... ... ... ... ... ... ..T ... ..A ... ... ... ..C ... ... ... ... ..C ... ... T.. G.A A.. ... ... ... AA. ..T ... ... ... ... ... ... ..G ..G .C. ... ..C ... ..G ..T ... AG. ... ... ... ... ... ..A ... ..T .AG ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T AT. ... T.T ... ..T ... ... ... ... ..T ..T .AG ... ... ... ... ... ... ... ..T ..A ..C ... -rat ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ..T ..T ..C T.. G.. ..A ..T .CA .AC ..C ..A C.. ..T GGT ..C ... ... A.T ... ... ... ..T ..C ..G ..T ..T ..T ... ... ... T.. ..G ... ... ... T.. ..T TG. .A. ..T .GA ..T ... ..A ..C ..C A.. ... ... ..T ..T ..C ... ... ..T ... ..G ... ... ..A ... GA. .CT ... G.. ..T ... .A. ... ... ..A ... CCT ... ..T ... ... ..C ... ... ... ..T ... ... ... ... .A. ... ..T AG. ... ... ..C ... ... T.. G.C TC. ... A.C ... ..T ... ... ... ... ..C ... ... ..G A.A AAC ... ..C .A. ... ... ... AAA ... T.. ... ... ... ... ... ..T CAT ... ... ..A ... ..T ... ... ... ... ... ... ..T A.. A.T ..G AT. ... .G. ..C ... C.G ..G ... ... ... ..C TGT .CA ... ... .TC ... ..A .G. ..T ... ..C ... -marsupial ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... ..A ... ..T ..C ..T T.. C.G ..T ..T ..C C.. ... C.. ... GGA A.C A.. ... AAA ..A ... ... ... ..C ..G A.A ..T ..C ..G ... ... ... ..C TCT ... A.C ... ... ... ..G AG. AAG ..T ..G ..T ..C .AA ... ... ... ... T.T ..C ... GCT ... ..G ..G ... ... T.. ... T.. ... ... AAC TG. A.C ... A.. A.C TCT C.G ..T ..C C.G AC. ... ... ..T ... ..C ..T ... ..C ... ACC ..T ... .G. AG. ... ..T ... ... ... T.. ... .GC ... ..C ... TCA ..T T.. ..T C.A ..C ... GCT ..G T.G ACC T.. ..C G.. ..A .CA G.C AAG ..T T.. ... ... ..G ... .A. ... .AG T.. ... ... ... ..T ..C ... ... .A. A.G ..G ..T A.C A.T ..G ATC TGC ..T G.G ... ... ..G ..T ..T ..T ..T GA. TGT .T. ..T .GG C.C ..A C.. ... ... ..C ... - - 9 2 1 1 1 4 3 1 1 1 2 1 1 3 1 - 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 5 1 1 1 4 2 2 1 6 1 1 1 1 - 1 3 1 1 3 1 1 1 2 3 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 - 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 - 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 - 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 - 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 - -CODONML (in paml version 4, June 2007) abglobin.nuc Model: One dN/dS ratio -Codon frequencies: Fequal -ns = 5 ls = 285 - -Codon usage in sequences --------------------------------------------------------------------------------------------------- -Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 - TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 --------------------------------------------------------------------------------------------------- -Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 - CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 - CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 - CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 - ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 - ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 -Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 --------------------------------------------------------------------------------------------------- -Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 - GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 - GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 - GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: human -position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 -position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 -position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 -Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 - -#2: goat-cow -position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 -position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 -position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 -Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 - -#3: rabbit -position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 -position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 -position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 -Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 - -#4: rat -position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 -position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 -position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 -Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 - -#5: marsupial -position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 -position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 -position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 -Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 - TTC 51 | TCC 31 | TAC 19 | TGC 9 -Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 - TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------- -Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 - CTC 24 | CCC 25 | CAC 68 | CGC 1 - CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 - CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------- -Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 - ATC 12 | ACC 53 | AAC 35 | AGC 19 - ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 -Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------- -Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 - GTC 19 | GCC 92 | GAC 48 | GGC 60 - GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 - GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 -position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 -position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 -Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 - -Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.00000000 0.00000000 - 0.01639344 0.01639344 0.00000000 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - 0.01639344 0.01639344 0.01639344 0.01639344 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -human -goat-cow 0.2507 (0.0863 0.3443) -rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) -rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) -marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) - -pairwise comparison, codon frequencies: Fequal. - - -2 (goat-cow) ... 1 (human) -lnL =-1596.739984 - 0.43894 1.87997 0.29075 - -t= 0.4389 S= 236.2 N= 618.8 dN/dS= 0.2908 dN= 0.0874 dS= 0.3006 - - -3 (rabbit) ... 1 (human) -lnL =-1593.524138 - 0.43016 1.74883 0.29827 - -t= 0.4302 S= 234.0 N= 621.0 dN/dS= 0.2983 dN= 0.0872 dS= 0.2924 - - -3 (rabbit) ... 2 (goat-cow) -lnL =-1634.706680 - 0.49216 1.87718 0.33712 - -t= 0.4922 S= 236.1 N= 618.9 dN/dS= 0.3371 dN= 0.1063 dS= 0.3154 - - -4 (rat) ... 1 (human) -lnL =-1722.645692 - 0.71450 1.56250 0.22967 - -t= 0.7145 S= 230.6 N= 624.4 dN/dS= 0.2297 dN= 0.1250 dS= 0.5445 - - -4 (rat) ... 2 (goat-cow) -lnL =-1750.493581 - 0.75917 2.15224 0.28700 - -t= 0.7592 S= 240.3 N= 614.7 dN/dS= 0.2870 dN= 0.1490 dS= 0.5192 - - -4 (rat) ... 3 (rabbit) -lnL =-1730.718528 - 0.73744 1.94983 0.24972 - -t= 0.7374 S= 237.3 N= 617.7 dN/dS= 0.2497 dN= 0.1340 dS= 0.5368 - - -5 (marsupial) ... 1 (human) -lnL =-1854.925323 - 1.18627 1.01786 0.17389 - -t= 1.1863 S= 218.3 N= 636.7 dN/dS= 0.1739 dN= 0.1787 dS= 1.0276 - - -5 (marsupial) ... 2 (goat-cow) -lnL =-1853.486254 - 1.12573 1.26005 0.19796 - -t= 1.1257 S= 224.3 N= 630.7 dN/dS= 0.1980 dN= 0.1819 dS= 0.9189 - - -5 (marsupial) ... 3 (rabbit) -lnL =-1873.309372 - 1.18527 1.16455 0.20554 - -t= 1.1853 S= 222.0 N= 633.0 dN/dS= 0.2055 dN= 0.1972 dS= 0.9593 - - -5 (marsupial) ... 4 (rat) -lnL =-1901.596050 - 1.20106 1.12357 0.24932 - -t= 1.2011 S= 221.0 N= 634.0 dN/dS= 0.2493 dN= 0.2251 dS= 0.9030 diff --git a/t/data/codeml43.mlc b/t/data/codeml43.mlc deleted file mode 100644 index 81df32ec0..000000000 --- a/t/data/codeml43.mlc +++ /dev/null @@ -1,231 +0,0 @@ - -seed used = 738594397 - 5 855 - -human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC ACC ACC AAG ACC TAC TTC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG CAC GTG GAC GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC GAC CTG CAC GCG CAC AAG CTT CGG GTG GAC CCG GTC AAC TTC AAG CTC CTA AGC CAC TGC CTG CTG GTG ACC CTG GCC GCC CAC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GAC AAG TTC CTG GCT TCT GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG AAG TCT GCC GTT ACT GCC CTG TGG GGC AAG GTG AAC GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTG GTC TAC CCT TGG ACC CAG AGG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT AAG GTG AAG GCT CAT GGC AAG AAA GTG CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG GGC ACC TTT GCC ACA CTG AGT GAG CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTC TGT GTG CTG GCC CAT CAC TTT GGC AAA GAA TTC ACC CCA CCA GTG CAG GCT GCC TAT CAG AAA GTG GTG GCT GGT GTG GCT AAT GCC CTG GCC CAC AAG TAT CAC -goat-cow GTG CTG TCT GCC GCC GAC AAG TCC AAT GTC AAG GCC GCC TGG GGC AAG GTT GGC GGC AAC GCT GGA GCT TAT GGC GCA GAG GCT CTG GAG AGG ATG TTC CTG AGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC CTG AGC CAC GGC TCG GCC CAG GTC AAG GGC CAC GGC GAG AAG GTG GCC GCC GCG CTG ACC AAA GCG GTG GGC CAC CTG GAC GAC CTG CCC GGT ACT CTG TCT GAT CTG AGT GAC CTG CAC GCC CAC AAG CTG CGT GTG GAC CCG GTC AAC TTT AAG CTT CTG AGC CAC TCC CTG CTG GTG ACC CTG GCC TGC CAC CTC CCC AAT GAT TTC ACC CCC GCG GTC CAC GCC TCC CTG GAC AAG TTC TTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAC CGT CTG ACT GCT GAG GAG AAG GCT GCC GTC ACC GCC TTT TGG GGC AAG GTG AAA GTG GAT GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCC TGG ACT CAG AGG TTC TTT GAG TCC TTT GGG GAC TTG TCC ACT GCT GAT GCT GTT ATG AAC AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG CTA GAT TCC TTT AGT AAT GGC ATG AAG CAT CTC GAT GAC CTC AAG GGC ACC TTT GCT GCG CTG AGT GAG CTG CAC TGT GAT AAG CTG CAT GTG GAT CCT GAG AAC TTC AAG CTC CTG GGC AAC GTG CTA GTG GTT GTG CTG GCT CGC AAT TTT GGC AAG GAA TTC ACC CCG GTG CTG CAG GCT GAC TTT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCC CAC AGA TAT CAT -rabbit GTG CTG TCT CCC GCT GAC AAG ACC AAC ATC AAG ACT GCC TGG GAA AAG ATC GGC AGC CAC GGT GGC GAG TAT GGC GCC GAG GCC GTG GAG AGG ATG TTC TTG GGC TTC CCC ACC ACC AAG ACC TAC TTC CCC CAC TTC GAC TTC ACC CAC GGC TCT GAG CAG ATC AAA GCC CAC GGC AAG AAG GTG TCC GAA GCC CTG ACC AAG GCC GTG GGC CAC CTG GAC GAC CTG CCC GGC GCC CTG TCT ACT CTC AGC GAC CTG CAC GCG CAC AAG CTG CGG GTG GAC CCG GTG AAT TTC AAG CTC CTG TCC CAC TGC CTG CTG GTG ACC CTG GCC AAC CAC CAC CCC AGT GAA TTC ACC CCT GCG GTG CAT GCC TCC CTG GAC AAG TTC CTG GCC AAC GTG AGC ACC GTG CTG ACC TCC AAA TAT CGT CTG TCC AGT GAG GAG AAG TCT GCG GTC ACT GCC CTG TGG GGC AAG GTG AAT GTG GAA GAA GTT GGT GGT GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCA TGG ACC CAG AGG TTC TTC GAG TCC TTT GGG GAC CTG TCC TCT GCA AAT GCT GTT ATG AAC AAT CCT AAG GTG AAG GCT CAT GGC AAG AAG GTG CTG GCT GCC TTC AGT GAG GGT CTG AGT CAC CTG GAC AAC CTC AAA GGC ACC TTT GCT AAG CTG AGT GAA CTG CAC TGT GAC AAG CTG CAC GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAC GTG CTG GTT ATT GTG CTG TCT CAT CAT TTT GGC AAA GAA TTC ACT CCT CAG GTG CAG GCT GCC TAT CAG AAG GTG GTG GCT GGT GTG GCC AAT GCC CTG GCT CAC AAA TAC CAC -rat GTG CTC TCT GCA GAT GAC AAA ACC AAC ATC AAG AAC TGC TGG GGG AAG ATT GGT GGC CAT GGT GGT GAA TAT GGC GAG GAG GCC CTA CAG AGG ATG TTC GCT GCC TTC CCC ACC ACC AAG ACC TAC TTC TCT CAC ATT GAT GTA AGC CCC GGC TCT GCC CAG GTC AAG GCT CAC GGC AAG AAG GTT GCT GAT GCC TTG GCC AAA GCT GCA GAC CAC GTC GAA GAC CTG CCT GGT GCC CTG TCC ACT CTG AGC GAC CTG CAT GCC CAC AAA CTG CGT GTG GAT CCT GTC AAC TTC AAG TTC CTG AGC CAC TGC CTG CTG GTG ACC TTG GCT TGC CAC CAC CCT GGA GAT TTC ACA CCC GCC ATG CAC GCC TCT CTG GAC AAA TTC CTT GCC TCT GTG AGC ACT GTG CTG ACC TCC AAG TAC CGT CTA ACT GAT GCT GAG AAG GCT GCT GTT AAT GCC CTG TGG GGA AAG GTG AAC CCT GAT GAT GTT GGT GGC GAG GCC CTG GGC AGG CTG CTG GTT GTC TAC CCT TGG ACC CAG AGG TAC TTT GAT AGC TTT GGG GAC CTG TCC TCT GCC TCT GCT ATC ATG GGT AAC CCT AAG GTG AAG GCC CAT GGC AAG AAG GTG ATA AAC GCC TTC AAT GAT GGC CTG AAA CAC TTG GAC AAC CTC AAG GGC ACC TTT GCT CAT CTG AGT GAA CTC CAC TGT GAC AAG CTG CAT GTG GAT CCT GAG AAC TTC AGG CTC CTG GGC AAT ATG ATT GTG ATT GTG TTG GGC CAC CAC CTG GGC AAG GAA TTC ACC CCC TGT GCA CAG GCT GCC TTC CAG AAG GTG GTG GCT GGA GTG GCC AGT GCC CTG GCT CAC AAG TAC CAC -marsupial GTG CTC TCG GAT GCT GAC AAG ACT CAC GTG AAA GCC ATC TGG GGT AAG GTG GGA GGC CAC GCC GGT GCC TAC GCA GCT GAA GCT CTT GCC AGA ACC TTC CTC TCC TTC CCC ACT ACC AAA ACT TAC TTC CCC CAC TTC GAC CTG TCC CCC GGC TCC GCC CAG ATC CAG GGT CAT GGT AAG AAG GTA GCC GAT GCC CTT TCC CAG GCT GTT GCC CAC CTG GAC GAC CTG CCC GGA ACC ATG TCC AAA CTA AGC GAC CTG CAC GCC CAC AAG CTG AGA GTG GAT CCC GTG AAC TTC AAG CTC CTC TCT CAC TGC CTG ATC GTG ACT CTG GCC GCC CAT CTG AGC AAG GAT TTG ACT CCC GAA GTG CAC GCC TCC ATG GAC AAG TTC TTT GCC TCT GTG GCT ACC GTG CTG ACC TCG AAG TAC CGT TTG ACT TCT GAG GAG AAG AAC TGC ATC ACT ACC ATC TGG TCT AAG GTG CAG GTT GAC CAG ACT GGT GGT GAG GCC CTT GGC AGG ATG CTC GTT GTC TAC CCC TGG ACC ACC AGG TTT TTT GGG AGC TTT GGT GAT CTG TCC TCT CCT GGC GCT GTC ATG TCA AAT TCT AAG GTT CAA GCC CAT GGT GCT AAG GTG TTG ACC TCC TTC GGT GAA GCA GTC AAG CAT TTG GAC AAC CTG AAG GGT ACT TAT GCC AAG TTG AGT GAG CTC CAC TGT GAC AAG CTG CAT GTG GAC CCT GAG AAC TTC AAG ATG CTG GGG AAT ATC ATT GTG ATC TGC CTG GCT GAG CAC TTT GGC AAG GAT TTT ACT CCT GAA TGT CAG GTT GCT TGG CAG AAG CTC GTG GCT GGA GTT GCC CAT GCC CTG GCC CAC AAG TAC CAC - - - -Printing out site pattern counts - - - 5 669 P - -human AAA AAA AAA AAC AAC AAC AAC AAC AAC AAC AAC AAC AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT ACA ACC ACC ACC ACC ACC ACC ACC ACC ACT ACT ACT AGC AGC AGC AGC AGG AGG AGG AGT AGT ATG ATG ATG CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAG CAG CAT CAT CCA CCA CCC CCC CCC CCG CCG CCT CCT CCT CCT CCT CCT CCT CGG CGT CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTT GAA GAA GAC GAC GAC GAC GAC GAC GAG GAG GAG GAG GAG GAG GAG GAG GAT GAT GAT GAT GAT GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCG GCG GCG GCG GCG GCG GCG GCT GCT GCT GCT GCT GCT GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGG GGT GGT GGT GGT GGT GTC GTC GTC GTC GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTT GTT GTT GTT GTT TAC TAC TAT TAT TAT TCC TCC TCC TCC TCC TCC TCT TCT TCT TCT TGC TGG TGT TGT TTC TTC TTC TTC TTC TTC TTT TTT TTT TTT TTT -goat-cow ... ..G ..G ..A ..A ... ... ... ... ..T G.. GGT ... ... ... ... ... ... ... .GA G.. ... G.G ... ... ... ... ... ... ..T T.. ..C ... ... ... ... ... ..T .A. ... ... ... ... ... ... C.. A.. A.T ... ... ... ... ... ..T ..T ..T ... ... ... .GC ..G GTG ... ... ... ..C ... ..C ..C ... ... G.C G.. G.. ..T ... ..G ..A ... ... ... ..T A.. ..A ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. T.. T.T ..G ... ... ... ... ... ... ..T .C. ... ... ... ... ... ... ..T .CT A.. ..C ... ... ... AAT .A. .AT ... ... ... ... ... ... ... ... ... ... ..G ..T ..T ..T T.. TG. A.T ..A ..C ... ... .GC .GC AAG ..C ..C ... ... ... AA. ..A ... ... ... ... ... ... ... ... ... .A. ..C ... ... ... ... ... ... ..G C.. C.. ..C ... ... ... ... ... ... ... ... ..T ..C ..C ... ... ... ... ... ... ... .T. AG. ... ... ... ... ..T AAC G.. ..G ... .C. ... GT. ... ... ... ... ... ... ..T ... ... ... ... ... -rabbit ... ... ..G ..G ..T ... ... ..T ..T ... ... GG. ..A ..A ... ... ... ... ... ..A ... ... .AG ... ... ... ... ... ..T ... ... ... T.C T.. .C. ... TC. ... ... ... ... ... ... ... ... C.. ... ..T ... ... ... ... ..T ... ... ... ... ... ... ... ..T .AG ... ... ... ..C ... ..A ... ... ... ..C AG. G.A ... ... ..G ..G .A. ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... G.. T.C T.. ... ... ... ..G ... ... ... ... ... ... ... ..A ..A ... ... ... ... ... ..A ... ..G ..C A.. ..A ... AGT ... A.T A.T .AG ... ... ... ... ..G ..T ..T T.. ... ... ..T T.T ... AA. ..C ..C ... ..C ... AGC .GC AG. ..C ... ... ... .G. AA. ... .AA .C. ... ... ... ... ... ..T ... .C. ..C ... ... ... A.. ... ..G ..T C.. ... ... ... ... ... ... ... ... ... ... ..T A.C ..C A.C ... ... ... ..T ..C ... ... GG. ... ... ... ... ..T AAC ... ... ... ... ... AT. ... ... ... ... ... ... ... ..C ..C ... ... ... -rat ..G ..G ..G ..A ... ... ..T ... ... ... ... GGT ... ... ..A ... ... ... ... ... ... .G. CAT ..A ... ... ..T G.. ... ... ... .A. ... T.. ... ... ... ... ... ... ... .A. ... ... ... C.. ..T ... ... ... ..T .C. ... ... ... ..T ... ... ... ..C ..C TGT ... ..T ..T T.T ..T ... ..C ... ... G.A GA. G.C ..T ... ..G A.A .A. ... ... T.. ... A.T T.. ... ..A ..C ... ... ... ... ... ... T.. T.. ..A G.A GCT ... ..T ... ..G ... ..T ..A ... ..T ..T ... ..T ..A C.. ... ... ..T .CT ..T ..A ... ..C TC. ... ... .GA ... A.T AA. ... ... ... ..T TG. ..T .AT ..T ..T ..T ... ..T .G. ... TG. ..C .A. ..C ..C ..C .GC .AC AAA ..C ..C ... ... .G. ..T ..T ..G .CT ..A ... ... ... ..T ... ... AAC ..C ..A ..C ... A.. ... ... ..G ..C .CA A.. A.. CCT .CA ... ... ... ... ..T ..T ..C ... A.. A.C ... ... ... ..C ... .TC G.. AG. ... ... ..T ... ... G.. ... ... ... ... AT. ... A.T .A. ... ... ... ... ..C ... C.G ... ... -marsupial ..G ..G ..G C.G C.G ... ..T ... ..T C.. ... GGA ... C.. ... ..A ... C.A GCT ... ... C.. .AG ..T ... ..T ... T.. ..T ... ..T ... ... T.. TC. GCT TCT ... .A. ..A ... G.. ... .CC ... C.. ... ... ... ..T ... .C. ... ... ..T ..T ACC ... ... G.G ..T GA. ... AG. ... ..C ..C ..C ..C ... T.. GA. T.. ... A.A ... ..C T.G ..G A.G ..G ... G.C A.T T.. ..A T.. ..C A.C A.. ..C ... ..T T.. ... ..T ..T ... ..C ... T.T A.C ..G ..T C.G ... ... ... ..T ... ..T ... .CC ..A ... .G. ... ..T .CC ..A ... .GC ..C ..C AAG ..T AAA ... ... A.. ... ... AT. TG. ..T ... ... ..T ..T ... ..T T.. ... A.C ..T ..C ..C .AA .GC ..C AAG ..C ..C ... .T. ..C TCA ..T ..T ..T TCT ... ..G ..T ..A .CA ..T ACC .CA ..A ... ... ..G ... ..G ..G C.. TGT ... A.C ..T ..T C.C ... ..T TGC ..A ..T A.C A.C ..G ..C AC. ... ... ..C ..C .GG ... AG. ... ..G ... ... ... AAC ..C ..G ... ... ATC ... ... ..T ... ..G ..T ... ..C ... ... .A. ... - - 1 1 2 1 1 1 1 1 1 1 1 1 1 1 3 - 2 7 1 1 1 1 1 1 1 2 4 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 - 1 1 1 6 2 1 1 1 1 1 1 1 3 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3 - 1 6 1 1 2 1 1 1 1 1 1 1 1 1 1 - 1 4 1 1 2 1 1 1 1 3 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 2 1 2 1 1 1 1 1 1 1 3 1 3 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 9 2 1 1 1 1 1 1 1 1 2 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 - 1 1 1 1 5 1 1 1 1 1 1 1 1 - -CODONML (in paml version 4.3, August 2009) abglobin.nuc -Model: One dN/dS ratio for branches -Codon frequency model: F3x4 -ns = 5 ls = 285 - -Codon usage in sequences --------------------------------------------------------------------------------------------------- -Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 - TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 --------------------------------------------------------------------------------------------------- -Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 - CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 - CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 - CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 - ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 - ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 -Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 --------------------------------------------------------------------------------------------------- -Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 - GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 - GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 - GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: human -position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 -position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 -position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 -Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 - -#2: goat-cow -position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 -position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 -position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 -Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 - -#3: rabbit -position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 -position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 -position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 -Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 - -#4: rat -position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 -position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 -position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 -Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 - -#5: marsupial -position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 -position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 -position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 -Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 - TTC 51 | TCC 31 | TAC 19 | TGC 9 -Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 - TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------- -Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 - CTC 24 | CCC 25 | CAC 68 | CGC 1 - CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 - CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------- -Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 - ATC 12 | ACC 53 | AAC 35 | AGC 19 - ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 -Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------- -Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 - GTC 19 | GCC 92 | GAC 48 | GGC 60 - GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 - GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 -position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 -position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 -Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 - -Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): - 0.00983798 0.01745548 0.00222048 0.01443315 - 0.00844604 0.01498576 0.00190632 0.01239105 - 0.01064012 0.01887870 0.00000000 0.00000000 - 0.00469486 0.00833007 0.00000000 0.00688776 - 0.01592816 0.02826125 0.00359507 0.02336796 - 0.01367453 0.02426265 0.00308642 0.02006170 - 0.01722686 0.03056552 0.00388819 0.02527326 - 0.00760121 0.01348678 0.00171563 0.01115161 - 0.01574077 0.02792876 0.00355278 0.02309304 - 0.01351366 0.02397721 0.00305010 0.01982568 - 0.01702419 0.03020593 0.00384245 0.02497593 - 0.00751178 0.01332811 0.00169545 0.01102042 - 0.02525082 0.04480239 0.00569924 0.03704508 - 0.02167816 0.03846344 0.00489288 0.03180369 - 0.02730964 0.04845534 0.00616393 0.04006555 - 0.01205015 0.02138052 0.00271978 0.01767859 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -human -goat-cow 0.2507 (0.0863 0.3443) -rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) -rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) -marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) - -pairwise comparison, codon frequencies: F3x4. - - -2 (goat-cow) ... 1 (human) -lnL =-1508.607268 - 0.47825 2.29137 0.19479 - -t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309 - - -3 (rabbit) ... 1 (human) -lnL =-1512.583367 - 0.46755 2.19039 0.19819 - -t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247 - - -3 (rabbit) ... 2 (goat-cow) -lnL =-1557.337680 - 0.53837 2.26427 0.22670 - -t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570 - - -4 (rat) ... 1 (human) -lnL =-1649.727994 - 0.82576 1.78920 0.15108 - -t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097 - - -4 (rat) ... 2 (goat-cow) -lnL =-1677.101606 - 0.88091 2.40576 0.18757 - -t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773 - - -4 (rat) ... 3 (rabbit) -lnL =-1666.440696 - 0.85281 2.21652 0.16114 - -t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105 - - -5 (marsupial) ... 1 (human) -lnL =-1769.079306 - 2.29076 0.98664 0.05689 - -t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396 - - -5 (marsupial) ... 2 (goat-cow) -lnL =-1774.766235 - 1.80490 1.19637 0.08052 - -t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879 - - -5 (marsupial) ... 3 (rabbit) -lnL =-1794.595175 - 2.09984 1.06589 0.06930 - -t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162 - - -5 (marsupial) ... 4 (rat) -lnL =-1842.638722 - 1.66307 1.02118 0.12318 - -t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973 diff --git a/t/data/codeml43_nssites.mlc b/t/data/codeml43_nssites.mlc deleted file mode 100644 index 58c228e95..000000000 --- a/t/data/codeml43_nssites.mlc +++ /dev/null @@ -1,251 +0,0 @@ - -seed used = 739250845 -CODONML (in paml version 4.3, August 2009) abglobin.nuc -Model: One dN/dS ratio for branches -Codon frequency model: F3x4 -Site-class models: -ns = 5 ls = 285 - -Codon usage in sequences --------------------------------------------------------------------------------------------------- -Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 - TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 --------------------------------------------------------------------------------------------------- -Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 - CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 - CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 - CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 - ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 - ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 -Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 --------------------------------------------------------------------------------------------------- -Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 - GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 - GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 - GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: human -position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 -position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 -position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 -Average T:0.20468 C:0.31345 A:0.18480 G:0.29708 - -#2: goat-cow -position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 -position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 -position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 -Average T:0.21988 C:0.29123 A:0.19181 G:0.29708 - -#3: rabbit -position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 -position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 -position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 -Average T:0.21053 C:0.29708 A:0.20819 G:0.28421 - -#4: rat -position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 -position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 -position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 -Average T:0.22924 C:0.28421 A:0.21404 G:0.27251 - -#5: marsupial -position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 -position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 -position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 -Average T:0.24211 C:0.29240 A:0.20585 G:0.25965 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8 - TTC 51 | TCC 31 | TAC 19 | TGC 9 -Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0 - TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16 ------------------------------------------------------------------------------- -Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7 - CTC 24 | CCC 25 | CAC 68 | CGC 1 - CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0 - CTG 123 | CCG 5 | CAG 25 | CGG 2 ------------------------------------------------------------------------------- -Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13 - ATC 12 | ACC 53 | AAC 35 | AGC 19 - ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3 -Met M ATG 17 | ACG 0 | AAG 98 | AGG 17 ------------------------------------------------------------------------------- -Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30 - GTC 19 | GCC 92 | GAC 48 | GGC 60 - GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7 - GTG 89 | GCG 14 | GAG 40 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 -position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 -position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 -Average T:0.22129 C:0.29567 A:0.20094 G:0.28211 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -human -goat-cow 0.2507 (0.0863 0.3443) -rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581) -rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187) -marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852) - - -Model 1: NearlyNeutral (2 categories) - - -TREE # 1: (((3, 4), 1), 2, 5); MP score: 387 -lnL(ntime: 7 np: 10): -2970.527521 +0.000000 - 6..7 7..8 8..3 8..4 7..1 6..2 6..5 - 0.081884 0.073268 0.252707 0.649536 0.215600 0.223230 1.401893 2.066843 0.826211 0.065970 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 2.89812 - -(((3: 0.252707, 4: 0.649536): 0.073268, 1: 0.215600): 0.081884, 2: 0.223230, 5: 1.401893); - -(((rabbit: 0.252707, rat: 0.649536): 0.073268, human: 0.215600): 0.081884, goat-cow: 0.223230, marsupial: 1.401893); - -Detailed output identifying parameters - -kappa (ts/tv) = 2.06684 - - -dN/dS (w) for site classes (K=2) - -p: 0.82621 0.17379 -w: 0.06597 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.082 663.8 191.2 0.2283 0.0155 0.0681 10.3 13.0 - 7..8 0.073 663.8 191.2 0.2283 0.0139 0.0609 9.2 11.7 - 8..3 0.253 663.8 191.2 0.2283 0.0480 0.2101 31.8 40.2 - 8..4 0.650 663.8 191.2 0.2283 0.1233 0.5401 81.8 103.3 - 7..1 0.216 663.8 191.2 0.2283 0.0409 0.1793 27.2 34.3 - 6..2 0.223 663.8 191.2 0.2283 0.0424 0.1856 28.1 35.5 - 6..5 1.402 663.8 191.2 0.2283 0.2661 1.1656 176.6 222.9 - - -Naive Empirical Bayes (NEB) analysis -Time used: 0:08 - - -Model 2: PositiveSelection (3 categories) - - -TREE # 1: (((3, 4), 1), 2, 5); MP score: 387 -lnL(ntime: 7 np: 12): -2965.809712 +0.000000 - 6..7 7..8 8..3 8..4 7..1 6..2 6..5 - 0.100782 0.089538 0.293059 0.801779 0.242098 0.264641 1.797878 2.181363 0.833468 0.136461 0.072723 6.285989 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 3.58978 - -(((3: 0.293059, 4: 0.801779): 0.089538, 1: 0.242098): 0.100782, 2: 0.264641, 5: 1.797878); - -(((rabbit: 0.293059, rat: 0.801779): 0.089538, human: 0.242098): 0.100782, goat-cow: 0.264641, marsupial: 1.797878); - -Detailed output identifying parameters - -kappa (ts/tv) = 2.18136 - - -dN/dS (w) for site classes (K=3) - -p: 0.83347 0.13646 0.03007 -w: 0.07272 1.00000 6.28599 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 6..7 0.101 662.3 192.7 0.3861 0.0247 0.0641 16.4 12.3 - 7..8 0.090 662.3 192.7 0.3861 0.0220 0.0569 14.6 11.0 - 8..3 0.293 662.3 192.7 0.3861 0.0719 0.1863 47.6 35.9 - 8..4 0.802 662.3 192.7 0.3861 0.1968 0.5096 130.3 98.2 - 7..1 0.242 662.3 192.7 0.3861 0.0594 0.1539 39.4 29.6 - 6..2 0.265 662.3 192.7 0.3861 0.0649 0.1682 43.0 32.4 - 6..5 1.798 662.3 192.7 0.3861 0.4412 1.1428 292.2 220.2 - - -Naive Empirical Bayes (NEB) analysis -Positively selected sites (*: P>95%; **: P>99%) -(amino acids refer to 1st sequence: human) - - Pr(w>1) post mean +- SE for w - - 35 S 0.643 4.400 - 111 A 0.736 4.890 - 115 A 0.785 5.151 - 131 S 0.704 4.722 - 144 P 0.794 5.198 - 215 A 0.799 5.225 - 226 T 0.560 3.962 - 264 P 0.971* 6.134 - - -Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) -Positively selected sites (*: P>95%; **: P>99%) -(amino acids refer to 1st sequence: human) - - Pr(w>1) post mean +- SE for w - - 35 S 0.634 4.600 +- 3.257 - 111 A 0.727 5.133 +- 3.164 - 115 A 0.779 5.538 +- 3.111 - 131 S 0.706 5.170 +- 3.273 - 144 P 0.781 5.485 +- 3.082 - 195 G 0.502 3.842 +- 3.253 - 215 A 0.788 5.577 +- 3.082 - 226 T 0.572 4.307 +- 3.325 - 264 P 0.964* 6.573 +- 2.443 - - - -The grid (see ternary graph for p0-p1) - -w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 -w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 - - -Posterior on the grid - -w0: 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -w2: 0.006 0.033 0.085 0.129 0.147 0.146 0.135 0.121 0.106 0.092 - -Posterior for p0-p1 (see the ternary graph) - - 0.000 - 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.199 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.100 0.700 - 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 - -sum of density on p0-p1 = 1.000000 - -Time used: 0:26 - -Time used: 0:26 diff --git a/t/data/codeml45.mlc b/t/data/codeml45.mlc deleted file mode 100644 index a5dcdabe0..000000000 --- a/t/data/codeml45.mlc +++ /dev/null @@ -1,460 +0,0 @@ - 9 1425 - -Pdel181_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -Pfre186_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -Pgra187_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATT GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATA AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG -Phet26_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -Pmex37_DNA21 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -Ptre197_DNA2 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCT GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG -WHR1_DNA225 ATG TCA CCA CAA ACA GAG ACT AAA GCG GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCC GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -YALD273_DNA5 ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG -Pop_trich_ch ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG - - - -Printing out site pattern counts - - - 9 225 P - -Pdel181_DNA2 AAA AAC AAG AAT ACA ACA ACC ACG ACT ACT AGA AGC AGG AGT ATA ATC ATC ATC ATG ATG ATT ATT CAA CAA CAC CAG CAT CCA CCC CCC CCG CCT CCT CGA CGC CGT CTA CTG CTG CTT GAA GAC GAG GAG GAT GCA GCC GCC GCT GCT GGA GGC GGG GGT GTA GTA GTC GTG GTT GTT GTT TAC TAT TCA TCC TCG TCT TCT TGC TGG TGT TTA TTC TTG TTT -Pfre186_DNA2 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -Pgra187_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ..T ..A ... ..A ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -Phet26_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -Pmex37_DNA21 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -Ptre197_DNA2 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..T A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -WHR1_DNA225 ... ... ... ... ... G.G ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... -YALD273_DNA5 ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -Pop_trich_ch ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... - - 18 6 6 9 5 1 8 1 16 1 6 3 1 1 1 - 7 1 1 1 9 1 9 9 1 5 2 9 3 5 1 - 2 1 10 6 5 11 9 1 3 9 24 5 1 9 22 - 15 4 1 1 23 13 2 9 23 1 12 1 4 1 1 - 13 4 13 1 4 1 1 5 3 8 5 9 8 10 14 - - -CODONML (in paml version 4.5, December 2011) examples/small_taxon_set.nuc -Model: One dN/dS ratio for branches -Codon frequency model: F3x4 -ns = 9 ls = 475 - -Codon usage in sequences --------------------------------------------------------------------------------------------------------------- -Phe TTT 14 14 14 14 14 14 | Ser TCT 6 6 6 6 6 6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT 5 5 5 5 5 5 - TTC 8 8 8 8 8 8 | TCC 4 4 4 4 4 4 | TAC 4 4 4 4 4 4 | TGC 3 3 3 3 3 3 -Leu TTA 9 9 9 9 9 9 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 - TTG 10 10 10 10 10 10 | TCG 1 1 1 1 1 1 | TAG 0 0 0 0 0 0 | Trp TGG 8 8 8 8 8 8 --------------------------------------------------------------------------------------------------------------- -Leu CTT 9 9 9 9 9 9 | Pro CCT 11 11 12 11 10 12 | His CAT 9 9 9 9 9 9 | Arg CGT 11 11 11 11 11 11 - CTC 0 0 0 0 0 0 | CCC 6 6 5 6 6 5 | CAC 5 5 5 5 5 5 | CGC 5 5 5 5 5 5 - CTA 9 9 9 10 9 9 | CCA 3 3 3 3 3 3 | Gln CAA 10 10 9 10 10 9 | CGA 6 6 6 6 6 6 - CTG 4 4 4 3 4 4 | CCG 2 2 2 2 2 2 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT 9 9 9 9 9 9 | Ser AGT 1 1 2 2 2 2 - ATC 9 9 7 9 9 8 | ACC 8 8 8 8 8 8 | AAC 6 6 6 6 6 6 | AGC 3 3 3 3 3 3 - ATA 1 1 4 2 1 3 | ACA 6 6 5 5 5 5 | Lys AAA 18 18 18 18 18 18 | Arg AGA 6 6 6 6 6 6 -Met ATG 10 10 10 9 10 10 | ACG 1 1 1 1 1 1 | AAG 6 6 6 6 6 6 | AGG 1 1 1 1 1 1 --------------------------------------------------------------------------------------------------------------- -Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23 - GTC 1 1 1 1 1 1 | GCC 5 5 5 5 5 4 | GAC 5 5 6 6 6 6 | GGC 2 2 2 2 2 2 - GTA 13 13 12 13 13 12 | GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 | GGA 13 13 13 13 13 13 - GTG 4 4 4 4 4 4 | GCG 0 0 0 0 0 0 | GAG 10 10 9 9 9 9 | GGG 9 9 9 9 9 9 --------------------------------------------------------------------------------------------------------------- - --------------------------------------------------------------------------- -Phe TTT 14 14 14 | Ser TCT 5 6 6 | Tyr TAT 13 13 13 | Cys TGT 5 5 5 - TTC 8 8 8 | TCC 5 4 4 | TAC 4 4 4 | TGC 3 3 3 -Leu TTA 9 9 9 | TCA 1 1 1 | *** TAA 0 0 0 | *** TGA 0 0 0 - TTG 10 10 10 | TCG 1 1 1 | TAG 0 0 0 | Trp TGG 8 8 8 --------------------------------------------------------------------------- -Leu CTT 9 9 9 | Pro CCT 10 11 11 | His CAT 9 9 9 | Arg CGT 11 11 11 - CTC 0 0 0 | CCC 6 6 6 | CAC 5 5 5 | CGC 5 5 5 - CTA 9 10 10 | CCA 3 3 3 | Gln CAA 10 10 10 | CGA 6 6 6 - CTG 4 3 3 | CCG 2 2 2 | CAG 2 2 2 | CGG 0 0 0 --------------------------------------------------------------------------- -Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT 9 9 9 | Ser AGT 2 2 2 - ATC 8 9 9 | ACC 8 8 8 | AAC 6 6 6 | AGC 3 3 3 - ATA 2 2 2 | ACA 5 5 5 | Lys AAA 18 18 18 | Arg AGA 6 6 6 -Met ATG 10 9 9 | ACG 1 1 1 | AAG 6 6 6 | AGG 1 1 1 --------------------------------------------------------------------------- -Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23 - GTC 1 1 1 | GCC 5 5 5 | GAC 5 6 6 | GGC 2 2 2 - GTA 13 13 13 | GCA 15 16 16 | Glu GAA 24 24 24 | GGA 13 13 13 - GTG 4 4 4 | GCG 1 0 0 | GAG 10 9 9 | GGG 9 9 9 --------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: Pdel181_DNA2 -position 1: T:0.18105 C:0.19368 A:0.23579 G:0.38947 -position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 -position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 -Average T:0.28842 C:0.19368 A:0.27298 G:0.24491 - -#2: Pfre186_DNA2 -position 1: T:0.18105 C:0.19368 A:0.23789 G:0.38737 -position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 -position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 -Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 - -#3: Pgra187_DNA2 -position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 -position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 -position 3: T:0.42105 C:0.15158 A:0.28632 G:0.14105 -Average T:0.28842 C:0.19158 A:0.27579 G:0.24421 - -#4: Phet26_DNA21 -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 -Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 - -#5: Pmex37_DNA21 -position 1: T:0.18105 C:0.19158 A:0.23789 G:0.38947 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28211 G:0.14105 -Average T:0.28842 C:0.19298 A:0.27368 G:0.24491 - -#6: Ptre197_DNA2 -position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 -position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 -position 3: T:0.42316 C:0.15158 A:0.28421 G:0.14105 -Average T:0.28912 C:0.19158 A:0.27509 G:0.24421 - -#7: WHR1_DNA225 -position 1: T:0.18105 C:0.19158 A:0.23579 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41684 C:0.15579 A:0.28211 G:0.14526 -Average T:0.28772 C:0.19228 A:0.27298 G:0.24702 - -#8: YALD273_DNA5 -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 -Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 - -#9: Pop_trich_ch -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 -Average T:0.28842 C:0.19368 A:0.27368 G:0.24421 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 126 | Ser S TCT 53 | Tyr Y TAT 117 | Cys C TGT 45 - TTC 72 | TCC 37 | TAC 36 | TGC 27 -Leu L TTA 81 | TCA 9 | *** * TAA 0 | *** * TGA 0 - TTG 90 | TCG 9 | TAG 0 | Trp W TGG 72 ------------------------------------------------------------------------------- -Leu L CTT 81 | Pro P CCT 99 | His H CAT 81 | Arg R CGT 99 - CTC 0 | CCC 52 | CAC 45 | CGC 45 - CTA 84 | CCA 27 | Gln Q CAA 88 | CGA 54 - CTG 33 | CCG 18 | CAG 18 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 92 | Thr T ACT 152 | Asn N AAT 81 | Ser S AGT 16 - ATC 77 | ACC 72 | AAC 54 | AGC 27 - ATA 18 | ACA 47 | Lys K AAA 162 | Arg R AGA 54 -Met M ATG 87 | ACG 9 | AAG 54 | AGG 9 ------------------------------------------------------------------------------- -Val V GTT 131 | Ala A GCT 215 | Asp D GAT 198 | Gly G GGT 207 - GTC 9 | GCC 44 | GAC 51 | GGC 18 - GTA 115 | GCA 141 | Glu E GAA 218 | GGA 117 - GTG 36 | GCG 1 | GAG 84 | GGG 81 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.18105 C:0.19275 A:0.23649 G:0.38971 -position 2: T:0.26480 C:0.23041 A:0.30105 G:0.20374 -position 3: T:0.41942 C:0.15579 A:0.28421 G:0.14058 -Average T:0.28842 C:0.19298 A:0.27392 G:0.24468 - -Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): - 0.02080748 0.00772882 0.01409988 0.00697451 - 0.01810545 0.00672517 0.01226889 0.00606881 - 0.02365656 0.00878710 0.00000000 0.00000000 - 0.01601000 0.00594683 0.00000000 0.00536643 - 0.02215163 0.00822810 0.01501073 0.00742506 - 0.01927505 0.00715961 0.01306145 0.00646085 - 0.02518476 0.00935474 0.01706608 0.00844174 - 0.01704423 0.00633099 0.01154977 0.00571310 - 0.02717876 0.01009540 0.01841729 0.00911012 - 0.02364937 0.00878443 0.01602564 0.00792709 - 0.03090024 0.01147772 0.02093909 0.01035753 - 0.02091228 0.00776775 0.01417090 0.00700964 - 0.04478716 0.01663594 0.03034936 0.01501232 - 0.03897116 0.01447562 0.02640823 0.01306284 - 0.05091968 0.01891383 0.03450497 0.01706789 - 0.03446079 0.01280027 0.02335185 0.01155100 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later ML. analysis. -Use runmode = -2 for ML pairwise comparison.) - -Pdel181_DNA2 -Pfre186_DNA2 -1.0000 (0.0009 0.0000) -Pgra187_DNA2 1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088) -Phet26_DNA21 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117) -Pmex37_DNA21 -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029) -Ptre197_DNA2 1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058) -WHR1_DNA225 0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117) -YALD273_DNA5 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088) -Pop_trich_ch 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000) - -pairwise comparison, codon frequencies: F3x4. - - -2 (Pfre186_DNA2) ... 1 (Pdel181_DNA2) -lnL =-1891.391969 - 0.00214 999.00000 99.00000 - -t= 0.0021 S= 396.3 N= 1028.7 dN/dS= 99.0000 dN = 0.0010 dS = 0.0000 - - -3 (Pgra187_DNA2) ... 1 (Pdel181_DNA2) -lnL =-1968.029688 - 0.02808 3.26389 0.98370 - -t= 0.0281 S= 341.7 N= 1083.3 dN/dS= 0.9837 dN = 0.0093 dS = 0.0095 - - -3 (Pgra187_DNA2) ... 2 (Pfre186_DNA2) -lnL =-1972.711786 - 0.03025 3.71696 1.10191 - -t= 0.0302 S= 345.4 N= 1079.6 dN/dS= 1.1019 dN = 0.0103 dS = 0.0094 - - -4 (Phet26_DNA21) ... 1 (Pdel181_DNA2) -lnL =-1921.561815 - 0.01073 3.11375 1.18654 - -t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 - - -4 (Phet26_DNA21) ... 2 (Pfre186_DNA2) -lnL =-1927.106138 - 0.01287 4.25522 1.54964 - -t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 - - -4 (Phet26_DNA21) ... 3 (Pgra187_DNA2) -lnL =-1948.501568 - 0.02179 4.30601 0.45869 - -t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 - - -5 (Pmex37_DNA21) ... 1 (Pdel181_DNA2) -lnL =-1920.298777 - 0.01053 1.55733 99.00000 - -t= 0.0105 S= 318.9 N= 1106.1 dN/dS= 99.0000 dN = 0.0045 dS = 0.0000 - - -5 (Pmex37_DNA21) ... 2 (Pfre186_DNA2) -lnL =-1914.616800 - 0.00838 0.77696 99.00000 - -t= 0.0084 S= 296.5 N= 1128.5 dN/dS= 99.0000 dN = 0.0035 dS = 0.0000 - - -5 (Pmex37_DNA21) ... 3 (Pgra187_DNA2) -lnL =-1960.971487 - 0.02594 4.03558 0.91514 - -t= 0.0259 S= 348.1 N= 1076.9 dN/dS= 0.9151 dN = 0.0085 dS = 0.0092 - - -5 (Pmex37_DNA21) ... 4 (Phet26_DNA21) -lnL =-1913.389962 - 0.00862 6.08298 0.97563 - -t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 - - -6 (Ptre197_DNA2) ... 1 (Pdel181_DNA2) -lnL =-1961.098136 - 0.02585 4.25957 1.53161 - -t= 0.0258 S= 349.5 N= 1075.5 dN/dS= 1.5316 dN = 0.0094 dS = 0.0061 - - -6 (Ptre197_DNA2) ... 2 (Pfre186_DNA2) -lnL =-1965.694050 - 0.02802 4.83643 1.71212 - -t= 0.0280 S= 352.8 N= 1072.2 dN/dS= 1.7121 dN = 0.0104 dS = 0.0061 - - -6 (Ptre197_DNA2) ... 3 (Pgra187_DNA2) -lnL =-1901.130192 - 0.00676 4.05781 0.00100 - -t= 0.0068 S= 345.2 N= 1079.8 dN/dS= 0.0010 dN = 0.0000 dS = 0.0093 - - -6 (Ptre197_DNA2) ... 4 (Phet26_DNA21) -lnL =-1941.618065 - 0.01954 6.78012 0.64571 - -t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 - - -6 (Ptre197_DNA2) ... 5 (Pmex37_DNA21) -lnL =-1953.852896 - 0.02372 5.63419 1.43296 - -t= 0.0237 S= 357.2 N= 1067.8 dN/dS= 1.4330 dN = 0.0086 dS = 0.0060 - - -7 (WHR1_DNA225) ... 1 (Pdel181_DNA2) -lnL =-1936.561781 - 0.01511 2.61161 0.72506 - -t= 0.0151 S= 337.6 N= 1087.4 dN/dS= 0.7251 dN = 0.0046 dS = 0.0064 - - -7 (WHR1_DNA225) ... 2 (Pfre186_DNA2) -lnL =-1941.975543 - 0.01725 3.35589 0.90347 - -t= 0.0172 S= 345.7 N= 1079.3 dN/dS= 0.9035 dN = 0.0056 dS = 0.0062 - - -7 (WHR1_DNA225) ... 3 (Pgra187_DNA2) -lnL =-1960.455637 - 0.02624 3.64066 0.41889 - -t= 0.0262 S= 345.9 N= 1079.1 dN/dS= 0.4189 dN = 0.0065 dS = 0.0156 - - -7 (WHR1_DNA225) ... 4 (Phet26_DNA21) -lnL =-1928.593448 - 0.01318 1.68562 0.26826 - -t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 - - -7 (WHR1_DNA225) ... 5 (Pmex37_DNA21) -lnL =-1928.718524 - 0.01300 3.82266 0.60956 - -t= 0.0130 S= 350.1 N= 1074.9 dN/dS= 0.6096 dN = 0.0037 dS = 0.0061 - - -7 (WHR1_DNA225) ... 6 (Ptre197_DNA2) -lnL =-1954.005346 - 0.02397 5.04975 0.54692 - -t= 0.0240 S= 355.1 N= 1069.9 dN/dS= 0.5469 dN = 0.0066 dS = 0.0121 - - -8 (YALD273_DNA5) ... 1 (Pdel181_DNA2) -lnL =-1921.561815 - 0.01073 3.11377 1.18654 - -t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 - - -8 (YALD273_DNA5) ... 2 (Pfre186_DNA2) -lnL =-1927.106138 - 0.01287 4.25516 1.54964 - -t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 - - -8 (YALD273_DNA5) ... 3 (Pgra187_DNA2) -lnL =-1948.501568 - 0.02179 4.30601 0.45869 - -t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 - - -8 (YALD273_DNA5) ... 4 (Phet26_DNA21) -lnL =-1881.846112 - 0.00001 8.33165 0.18598 - -t= 0.0000 S= 369.5 N= 1055.5 dN/dS= 0.1860 dN = 0.0000 dS = 0.0000 - - -8 (YALD273_DNA5) ... 5 (Pmex37_DNA21) -lnL =-1913.389962 - 0.00862 6.08296 0.97563 - -t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 - - -8 (YALD273_DNA5) ... 6 (Ptre197_DNA2) -lnL =-1941.618065 - 0.01954 6.78014 0.64571 - -t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 - - -8 (YALD273_DNA5) ... 7 (WHR1_DNA225) -lnL =-1928.593448 - 0.01318 1.68561 0.26826 - -t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 - - -9 (Pop_trich_ch) ... 1 (Pdel181_DNA2) -lnL =-1921.561815 - 0.01073 3.11378 1.18654 - -t= 0.0107 S= 342.5 N= 1082.5 dN/dS= 1.1865 dN = 0.0037 dS = 0.0031 - - -9 (Pop_trich_ch) ... 2 (Pfre186_DNA2) -lnL =-1927.106138 - 0.01287 4.25517 1.54964 - -t= 0.0129 S= 352.0 N= 1073.0 dN/dS= 1.5496 dN = 0.0047 dS = 0.0030 - - -9 (Pop_trich_ch) ... 3 (Pgra187_DNA2) -lnL =-1948.501568 - 0.02179 4.30599 0.45869 - -t= 0.0218 S= 349.8 N= 1075.2 dN/dS= 0.4587 dN = 0.0056 dS = 0.0123 - - -9 (Pop_trich_ch) ... 4 (Phet26_DNA21) -lnL =-1881.845859 - 0.00001 0.40000 0.00100 - -t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.0010 dN = 0.0000 dS = 0.0000 - - -9 (Pop_trich_ch) ... 5 (Pmex37_DNA21) -lnL =-1913.389962 - 0.00862 6.08299 0.97562 - -t= 0.0086 S= 362.3 N= 1062.7 dN/dS= 0.9756 dN = 0.0029 dS = 0.0029 - - -9 (Pop_trich_ch) ... 6 (Ptre197_DNA2) -lnL =-1941.618065 - 0.01954 6.78013 0.64571 - -t= 0.0195 S= 361.6 N= 1063.4 dN/dS= 0.6457 dN = 0.0057 dS = 0.0089 - - -9 (Pop_trich_ch) ... 7 (WHR1_DNA225) -lnL =-1928.593448 - 0.01318 1.68561 0.26826 - -t= 0.0132 S= 322.2 N= 1102.8 dN/dS= 0.2683 dN = 0.0027 dS = 0.0101 - - -9 (Pop_trich_ch) ... 8 (YALD273_DNA5) -lnL =-1881.846052 - 0.00001 0.40000 0.16519 - -t= 0.0000 S= 281.0 N= 1144.0 dN/dS= 0.1652 dN = 0.0000 dS = 0.0000 diff --git a/t/data/codeml_lysozyme/2NG.dN b/t/data/codeml_lysozyme/2NG.dN deleted file mode 100644 index 5ce212903..000000000 --- a/t/data/codeml_lysozyme/2NG.dN +++ /dev/null @@ -1,8 +0,0 @@ - 7 -Hsa_Human -Hla_gibbon 0.0133 -Cgu/Can_colobus 0.0742 0.0742 -Pne_langur 0.0725 0.0797 0.0267 -Mmu_rhesus 0.0562 0.0561 0.0473 0.0508 -Ssc_squirrelM 0.0633 0.0633 0.0775 0.0959 0.0559 -Cja_marmoset 0.0634 0.0633 0.0704 0.0886 0.0490 0.0099 diff --git a/t/data/codeml_lysozyme/2NG.dS b/t/data/codeml_lysozyme/2NG.dS deleted file mode 100644 index aa903eb9b..000000000 --- a/t/data/codeml_lysozyme/2NG.dS +++ /dev/null @@ -1,8 +0,0 @@ - 7 -Hsa_Human -Hla_gibbon 0.0478 -Cgu/Can_colobus 0.0670 0.0671 -Pne_langur 0.0605 0.0863 0.0484 -Mmu_rhesus 0.0300 0.0550 0.0364 0.0364 -Ssc_squirrelM 0.1346 0.1349 0.1502 0.1645 0.1230 -Cja_marmoset 0.1341 0.1069 0.1496 0.1638 0.1225 0.0619 diff --git a/t/data/codeml_lysozyme/2NG.tt b/t/data/codeml_lysozyme/2NG.tt deleted file mode 100644 index 0e111248f..000000000 --- a/t/data/codeml_lysozyme/2NG.tt +++ /dev/null @@ -1,8 +0,0 @@ - 7 -Hsa_Human -Hla_gibbon 0.0628 -Cgu/Can_colobus 0.2179 0.2179 -Pne_langur 0.2095 0.2435 0.0944 -Mmu_rhesus 0.1514 0.1676 0.1348 0.1430 -Ssc_squirrelM 0.2366 0.2366 0.2798 0.3324 0.2109 -Cja_marmoset 0.2366 0.2186 0.2628 0.3150 0.1944 0.0633 diff --git a/t/data/codeml_lysozyme/4fold.nuc b/t/data/codeml_lysozyme/4fold.nuc deleted file mode 100644 index 8ad8c2764..000000000 --- a/t/data/codeml_lysozyme/4fold.nuc +++ /dev/null @@ -1,26 +0,0 @@ - 7 38 - -Hsa_Human -CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG - -Hla_gibbon -CTGACAAACATAATGCCAAATCCTGTAATCACAGATAA - -Cgu/Can_colobus -CTGACAAACATAATGCCAAATCCTGTAATCACAGATAA - -Pne_langur -CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG - -Mmu_rhesus -CTGACAAACATAATGCCAAATCCTGTAATCACAGATAG - -Ssc_squirrelM -CTGACAAACATAATGCCAAATCCTGTGATCACAGATAA - -Cja_marmoset -CTGACAAACATAATGCCAAATCCTGTGATCACAGATAA - - -codons included - 9 11 12 16 19 22 25 26 32 40 42 43 48 52 55 68 70 71 72 73 74 76 80 83 85 92 93 96 99 100 103 105 108 110 111 127 129 130 diff --git a/t/data/codeml_lysozyme/lnf b/t/data/codeml_lysozyme/lnf deleted file mode 100644 index 9deb9edb0..000000000 --- a/t/data/codeml_lysozyme/lnf +++ /dev/null @@ -1,170 +0,0 @@ - 2 130 81 - - - 1 - - 1 2 -4.4631936441 1.4983 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) - 2 1 -9.5051356295 0.0097 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) - 3 1 -9.7022173688 0.0079 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) - 4 1 -4.2039253720 1.9418 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) - 5 2 -4.5556175232 1.3660 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) - 6 7 -4.3823910150 1.6244 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) - 7 2 -4.4321334372 1.5456 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) - 8 3 -5.0765672523 0.8114 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) - 9 3 -4.7615724447 1.1118 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) - 10 1 -4.3184529418 1.7317 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) - 11 2 -4.5084067380 1.4321 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) - 12 2 -5.4399561134 0.5642 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) - 13 2 -4.2372969984 1.8781 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) - 14 1 -10.9655217803 0.0022 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) - 15 1 -16.0576876241 0.0000 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) - 16 5 -4.3016142564 1.7611 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) - 17 1 -18.1074372042 0.0000 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) - 18 4 -4.1086751238 2.1358 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) - 19 3 -4.4725258929 1.4844 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) - 20 2 -4.5810698348 1.3317 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) - 21 1 -8.2006772519 0.0357 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) - 22 1 -8.6032910323 0.0239 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) - 23 3 -4.4856422368 1.4651 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) - 24 1 -5.2057180378 0.7131 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) - 25 5 -4.6403385123 1.2551 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) - 26 4 -4.4201645295 1.5642 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) - 27 5 -4.5973658698 1.3102 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) - 28 1 -9.7392781217 0.0077 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) - 29 1 -4.2139700025 1.9224 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) - 30 1 -19.3633273590 0.0000 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) - 31 1 -9.2797480927 0.0121 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) - 32 2 -4.6757503564 1.2114 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) - 33 1 -25.8812469730 0.0000 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) - 34 3 -4.4744717992 1.4815 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) - 35 2 -4.1412516220 2.0674 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) - 36 1 -11.8290710328 0.0009 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) - 37 1 -8.0038078071 0.0434 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) - 38 1 -19.2209541782 0.0000 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) - 39 1 -4.2784689093 1.8023 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) - 40 1 -4.5413001563 1.3857 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) - 41 1 -4.5300265454 1.4015 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) - 42 1 -4.6476460878 1.2459 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) - 43 2 -4.9562014725 0.9152 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) - 44 2 -4.6725375419 1.2153 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) - 45 1 -13.9526908087 0.0001 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) - 46 1 -7.7072272546 0.0584 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) - 47 1 -8.6619538016 0.0225 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) - 48 1 -7.6386523715 0.0626 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) - 49 1 -7.6180808245 0.0639 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) - 50 1 -4.7949680407 1.0753 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) - 51 2 -5.3234573070 0.6339 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) - 52 2 -4.3494722978 1.6788 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) - 53 1 -7.9306430266 0.0467 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) - 54 1 -4.6439287862 1.2506 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) - 55 1 -10.8202341235 0.0026 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) - 56 1 -5.0984488784 0.7938 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) - 57 1 -4.6812000239 1.2048 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) - 58 1 -12.7247989627 0.0004 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) - 59 3 -4.7045988601 1.1770 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) - 60 1 -11.0532635455 0.0021 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) - 61 1 -7.7553120801 0.0557 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) - 62 1 -12.8896050389 0.0003 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) - 63 1 -15.5069596712 0.0000 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) - 64 1 -8.1360516790 0.0381 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) - 65 1 -13.5299247810 0.0002 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) - 66 1 -4.6436582159 1.2509 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) - 67 1 -21.1344087505 0.0000 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) - 68 1 -8.6870212211 0.0219 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) - 69 1 -16.1125630985 0.0000 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) - 70 1 -4.7433920156 1.1322 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) - 71 1 -11.8747575648 0.0009 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) - 72 1 -18.5148919180 0.0000 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) - 73 1 -13.9739064280 0.0001 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) - 74 1 -8.4292988369 0.0284 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) - 75 1 -12.0273836865 0.0008 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) - 76 1 -10.1811649098 0.0049 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) - 77 1 -8.5983529672 0.0240 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) - 78 1 -9.0044467619 0.0160 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) - 79 1 -13.1118009094 0.0003 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) - 80 1 -4.1980256429 1.9533 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) - 81 1 -16.7711131668 0.0000 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) - - 2 - - 1 2 -4.4631960839 1.4983 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) - 2 1 -9.5051314395 0.0097 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) - 3 1 -9.7022223614 0.0079 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) - 4 1 -4.2039287045 1.9418 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) - 5 2 -4.5556198392 1.3660 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) - 6 7 -4.3823933327 1.6244 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) - 7 2 -4.4321358567 1.5456 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) - 8 3 -5.0765675735 0.8114 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) - 9 3 -4.7615736591 1.1118 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) - 10 1 -4.3184560927 1.7317 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) - 11 2 -4.5084089014 1.4321 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) - 12 2 -5.4399559761 0.5642 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) - 13 2 -4.2373003501 1.8781 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) - 14 1 -10.9655163954 0.0022 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) - 15 1 -16.0576801224 0.0000 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) - 16 5 -4.3016164401 1.7611 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) - 17 1 -18.1074279846 0.0000 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) - 18 4 -4.1086794471 2.1358 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) - 19 3 -4.4725278080 1.4844 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) - 20 2 -4.5810712480 1.3317 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) - 21 1 -8.2006676359 0.0357 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) - 22 1 -8.6032803791 0.0239 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) - 23 3 -4.4856451080 1.4650 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) - 24 1 -5.2057180047 0.7131 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) - 25 5 -4.6403399094 1.2551 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) - 26 4 -4.4201673653 1.5642 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) - 27 5 -4.5973665349 1.3102 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) - 28 1 -9.7392749110 0.0077 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) - 29 1 -4.2139743758 1.9224 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) - 30 1 -19.3632917534 0.0000 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) - 31 1 -9.2797457778 0.0121 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) - 32 2 -4.6757517792 1.2114 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) - 33 1 -25.8812555227 0.0000 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) - 34 3 -4.4744739440 1.4815 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) - 35 2 -4.1412559724 2.0674 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) - 36 1 -11.8290647008 0.0009 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) - 37 1 -8.0038170642 0.0434 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) - 38 1 -19.2209226010 0.0000 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) - 39 1 -4.2784711487 1.8023 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) - 40 1 -4.5413014475 1.3857 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) - 41 1 -4.5300288594 1.4014 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) - 42 1 -4.6476474833 1.2459 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) - 43 2 -4.9562019622 0.9151 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) - 44 2 -4.6725389296 1.2153 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) - 45 1 -13.9526618018 0.0001 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) - 46 1 -7.7072324162 0.0584 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) - 47 1 -8.6619636890 0.0225 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) - 48 1 -7.6386352162 0.0626 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) - 49 1 -7.6180754543 0.0639 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) - 50 1 -4.7949692808 1.0753 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) - 51 2 -5.3234581195 0.6339 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) - 52 2 -4.3494743162 1.6788 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) - 53 1 -7.9306463733 0.0467 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) - 54 1 -4.6439311725 1.2506 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) - 55 1 -10.8202230892 0.0026 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) - 56 1 -5.0984494878 0.7938 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) - 57 1 -4.6812015121 1.2048 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) - 58 1 -12.7247851075 0.0004 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) - 59 3 -4.7045995761 1.1770 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) - 60 1 -11.0532674855 0.0021 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) - 61 1 -7.7553062341 0.0557 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) - 62 1 -12.8895989932 0.0003 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) - 63 1 -15.5069647657 0.0000 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) - 64 1 -8.1360564354 0.0381 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) - 65 1 -13.5299179395 0.0002 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) - 66 1 -4.6436592953 1.2509 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) - 67 1 -21.1344217788 0.0000 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) - 68 1 -8.6870227601 0.0219 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) - 69 1 -16.1125651833 0.0000 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) - 70 1 -4.7433927068 1.1322 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) - 71 1 -11.8747461571 0.0009 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) - 72 1 -18.5148907665 0.0000 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) - 73 1 -13.9738939870 0.0001 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) - 74 1 -8.4293011794 0.0284 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) - 75 1 -12.0273822050 0.0008 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) - 76 1 -10.1811554378 0.0049 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) - 77 1 -8.5983668126 0.0240 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) - 78 1 -9.0044370152 0.0160 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) - 79 1 -13.1117968019 0.0003 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) - 80 1 -4.1980290700 1.9533 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) - 81 1 -16.7711243929 0.0000 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) \ No newline at end of file diff --git a/t/data/codeml_lysozyme/lysozymeSmall.ctl b/t/data/codeml_lysozyme/lysozymeSmall.ctl deleted file mode 100644 index fd001c833..000000000 --- a/t/data/codeml_lysozyme/lysozymeSmall.ctl +++ /dev/null @@ -1,37 +0,0 @@ - seqfile = lysozymeSmall.txt - treefile = lysozymeSmall.trees - outfile = mlc - - noisy = 9 * 0,1,2,3,9: how much rubbish on the screen - verbose = 1 * 1: detailed output, 0: concise output - runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic - * 3: StepwiseAddition; (4,5):PerturbationNNI - - seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs - CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table - model = 2 - * models for codons: - * 0:one, 1:b, 2:2 or more dN/dS ratios for branches - - NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive - icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below - - fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated - kappa = 2 * initial or fixed kappa - fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate - omega = 1 * initial or fixed omega, for codons or codon-transltd AAs - - fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha - alpha = .0 * initial or fixed alpha, 0:infinity (constant rate) - Malpha = 0 * different alphas for genes - ncatG = 4 * # of categories in the dG or AdG models of rates - - clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree - getSE = 0 * 0: don't want them, 1: want S.E.s of estimates - RateAncestor = 1 * (1/0): rates (alpha>0) or ancestral states (alpha=0) - method = 0 * 0: simultaneous; 1: one branch at a time - - -* Specifications for duplicating results for the small data set in table 1 -* of Yang (1998 MBE 15:568-573). -* see the tree file lysozyme.trees for specification of node (branch) labels diff --git a/t/data/codeml_lysozyme/lysozymeSmall.trees b/t/data/codeml_lysozyme/lysozymeSmall.trees deleted file mode 100644 index 1b61b0c98..000000000 --- a/t/data/codeml_lysozyme/lysozymeSmall.trees +++ /dev/null @@ -1,36 +0,0 @@ -2 - -((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, -((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254) #1 : 0.07637, Mmu_rhesus: -0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): -0.12266); -((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, -((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254) #1 : 0.07637, Mmu_rhesus: -0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): -0.12266); - - -((Hsa_Human, Hla_gibbon),((Cgu/Can_colobus, Pne_langur) #1, -Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); / * table 1B&F */ - - -((1,2), ((3,4) #1, 5), (6,7) ); / * table 1B&F */ -((1,2) #1, ((3,4), 5), (6,7) ); / * table 1C&G */ -((1,2) #1, ((3,4) #1, 5), (6,7) ); / * table 1D&H */ - -((1,2) #1, ((3,4) #2, 5), (6,7) ); / * table 1E&I */ -((1,2) #2, ((3,4) #1, 5), (6,7) ); / * table 1E&J */ - - -((1,2), ((3,4), 5), (6,7) ); - -For lysozymeSmall.nuc (Messier and Stewart 1997; Yang 1998) - - 1: Hsa_Human - 2: Hla_gibbon - 3: Cgu/Can_colobus - 4: Pne_langur - 5: Mmu_rhesus - 6: Ssc_squirrelM - 7: Cja_marmoset - diff --git a/t/data/codeml_lysozyme/lysozymeSmall.txt b/t/data/codeml_lysozyme/lysozymeSmall.txt deleted file mode 100644 index 06124648b..000000000 --- a/t/data/codeml_lysozyme/lysozymeSmall.txt +++ /dev/null @@ -1,64 +0,0 @@ - 7 390 - -Hsa_Human -AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGAATGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGGTTACAACACA -CGAGCTACAAACTACAATGCTGGAGACAGAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCC -TGCAGTGCTTTGCTGCAAGATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC -CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTCAAAACAGAGAT -GTCCGTCAGTATGTTCAAGGTTGTGGAGTG - -Hla_gibbon -AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGAATGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA -CGAGCTACAAACTACAATCCTGGAGACAGAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCC -TGCAATGCTTTGCTGCAAGATAACATCGCCGATGCTGTAGCTTGTGCAAAGAGGGTTGTC -CGCGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTCAAAACAGAGAT -CTCCGTCAGTATATTCAAGGTTGTGGAGTA - -Cgu/Can_colobus -AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAAATTGGGACTGGATGGCTAC -AAGGGAGTCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA -GACGCTACAAACTACAATCCTGGAGATGAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCGCTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC -TGCAATGCTTTGCTGCAAAATAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC -AGTGATCCACAAGGCATTCGAGCATGGGTGGCATGGAAAAAGCACTGTCAAAACAGAGAT -GTCAGTCAGTATGTTGAAGGTTGTGGAGTA - -Pne_langur -AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAAATTGGGACTGGATGGCTAC -AAGGGAGTCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTGGTTATAACACA -GAAGCTACAAACTACAATCCTGGAGACGAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCGCTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTGATGCCTGTCATATATCC -TGCAGTGCTTTGCTGCAAAACAACATCGCTGATGCTGTAGCTTGTGCAAAGAGGGTTGTC -AGTGATCCACAAGGCGTTCGAGCATGGGTGGCATGGAGAAATCACTGTCAAAACAAAGAT -GTCAGTCAGTACGTTAAAGGTTGTGGAGTG - -Mmu_rhesus -AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGATTGGGACTGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGGTGTGTTTGGCCAAATGGGAGAGTAATTATAACACA -CAAGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCACTACTGGTGTAATAATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATATATCC -TGCAATGCTTTGCTGCAAGATAACATCGCTGATGCTGTAACTTGTGCAAAGAGGGTTGTC -AGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCACTGTCAAAACAGAGAT -GTCAGTCAGTATGTTCAAGGTTGTGGAGTG - -Ssc_squirrelM -AAGGTCTTCGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGGCTTGGAATGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGACTATAACACA -CGTGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCACTATTGGTGTAATAATGGCAGAACCCCAGGAGCAGTTAATGCCTGTCATATATCC -TGCAATGCTTTGCTGCAAGATGACATCACTCAAGCTGTGGCCTGTGCAAAGAGGGTTGTC -CGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAAAGCTCATTGTCAAAACAGAGAT -GTCAGTCAGTATGTTCAAGGTTGTGGAGTA - -Cja_marmoset -AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACTCTGAAAAGGTTTGGACTGGATGGCTAC -AGGGGAATCAGCCTAGCAAACTGGATGTGTTTGGCCAAATGGGAGAGTGATTATAACACA -CGTGCTACAAACTACAATCCTGGAGACCAAAGCACTGATTATGGGATATTTCAGATCAAT -AGCCACTATTGGTGTAACAATGGCAGAACCCCAGGAGCAGTTAATGCCTGTCATATATCC -TGCAATGCTTTGCTGCAAGATGACATCACTGAAGCTGTGGCCTGTGCAAAGAGGGTTGTC -CGCGATCCACAAGGCATTAGGGCATGGGTGGCATGGAAAGCTCATTGTCAAAACAGAGAT -GTCAGTCAGTATGTTCAAGGTTGTGGAGTA diff --git a/t/data/codeml_lysozyme/mlc b/t/data/codeml_lysozyme/mlc deleted file mode 100644 index 829927ac7..000000000 --- a/t/data/codeml_lysozyme/mlc +++ /dev/null @@ -1,273 +0,0 @@ - -seed used = 162469585 - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - -CODONML (in paml 3.14, January 2004) lysozymeSmall.txt Model: several dN/dS ratios for branches -Codon frequencies: F3x4 - -ns = 7 ls = 130 -# site patterns = 81 - 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1 - 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1 - 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1 - 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 - -1 -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG -Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A -Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A -Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ... -Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ... -Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A -Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A - -Codon usage in sequences --------------------------------------------------------------------------------------------------------------- -Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7 - TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1 -Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 - TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5 --------------------------------------------------------------------------------------------------------------- -Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2 - CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0 - CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0 - CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2 - ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3 - ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4 -Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4 --------------------------------------------------------------------------------------------------------------- -Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1 - GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3 - GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5 - GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1 --------------------------------------------------------------------------------------------------------------- - --------------------------------------------------- -Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7 - TTC 0 | TCC 1 | TAC 2 | TGC 1 -Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0 - TTG 3 | TCG 0 | TAG 0 | Trp TGG 5 --------------------------------------------------- -Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1 - CTC 0 | CCC 0 | CAC 1 | CGC 1 - CTA 1 | CCA 2 | Gln CAA 5 | CGA 0 - CTG 3 | CCG 0 | CAG 2 | CGG 0 --------------------------------------------------- -Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2 - ATC 3 | ACC 1 | AAC 5 | AGC 3 - ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3 -Met ATG 1 | ACG 0 | AAG 2 | AGG 5 --------------------------------------------------- -Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1 - GTC 3 | GCC 4 | GAC 2 | GGC 3 - GTA 1 | GCA 5 | Glu GAA 2 | GGA 5 - GTG 2 | GCG 0 | GAG 2 | GGG 1 --------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: Hsa_Human -position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615 -position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#2: Hla_gibbon -position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308 -position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308 -position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462 - -#3: Cgu/Can_colobus -position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385 -position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#4: Pne_langur -position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154 -position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 -position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231 - -#5: Mmu_rhesus -position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538 -position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#6: Ssc_squirrelM -position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077 -position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 -position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231 - -#7: Cja_marmoset -position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846 -position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 -position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49 - TTC 1 | TCC 7 | TAC 21 | TGC 7 -Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35 ------------------------------------------------------------------------------- -Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8 - CTC 1 | CCC 0 | CAC 6 | CGC 6 - CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4 - CTG 18 | CCG 0 | CAG 14 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17 - ATC 22 | ACC 7 | AAC 35 | AGC 21 - ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28 -Met M ATG 7 | ACG 0 | AAG 17 | AGG 22 ------------------------------------------------------------------------------- -Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11 - GTC 19 | GCC 24 | GAC 10 | GGC 21 - GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35 - GTG 15 | GCG 0 | GAG 14 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846 -position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780 -position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231 - -Codon frequencies under model, for use in evolver: - 0.01378574 0.00962226 0.01059374 0.00809565 - 0.01181635 0.00824765 0.00908035 0.00693913 - 0.02279949 0.01591374 0.00000000 0.00000000 - 0.02052711 0.01432765 0.00000000 0.01205451 - 0.00941649 0.00657258 0.00723616 0.00552982 - 0.00807127 0.00563364 0.00620242 0.00473984 - 0.01557342 0.01087004 0.01196749 0.00914546 - 0.01402125 0.00978665 0.01077472 0.00823396 - 0.02214758 0.01545871 0.01701945 0.01300613 - 0.01898364 0.01325032 0.01458810 0.01114811 - 0.03662868 0.02556633 0.02814755 0.02151013 - 0.03297798 0.02301819 0.02534214 0.01936627 - 0.02320222 0.01619484 0.01782990 0.01362547 - 0.01988762 0.01388129 0.01528277 0.01167897 - 0.03837291 0.02678377 0.02948791 0.02253443 - 0.03454836 0.02411429 0.02654891 0.02028847 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -Hsa_Human -Hla_gibbon 0.2782 (0.0133 0.0478) -Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671) -Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484) -Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364) -Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230) -Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619) - - -TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 -lnL(ntime: 11 np: 14): -904.636553 +0.000000 - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.55906 - -((1: 0.025570, 2: 0.038929): 0.070000, ((3: 0.043878, 4: 0.052151): 0.079045, 5: 0.019487): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307); - -((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070000, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052151): 0.079045, Mmu_rhesus: 0.019487): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307); - -Detailed output identifying parameters - -kappa (ts/tv) = 4.56118 - -dN & dS for each branch - - branch t S N dN/dS dN dS S*dS N*dN - - 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8 - 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1 - 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2 - 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 - 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3 - 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 - 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4 - 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6 - 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1 - 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4 - 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0 - -tree length for dN: 0.17485 -tree length for dS: 0.21644 - -dS tree: -((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022498): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052332); -dN tree: -((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); - - - -TREE # 2: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 -lnL(ntime: 11 np: 14): -904.636553 -0.000000 - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.55906 - -((1: 0.025570, 2: 0.038929): 0.070001, ((3: 0.043878, 4: 0.052150): 0.079045, 5: 0.019488): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307); - -((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070001, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052150): 0.079045, Mmu_rhesus: 0.019488): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307); - -Detailed output identifying parameters - -kappa (ts/tv) = 4.56122 - -dN & dS for each branch - - branch t S N dN/dS dN dS S*dS N*dN - - 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8 - 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1 - 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2 - 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 - 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3 - 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7 - 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4 - 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6 - 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1 - 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4 - 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0 - -tree length for dN: 0.17485 -tree length for dS: 0.21644 - -dS tree: -((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022497): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052331); -dN tree: -((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005766): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); - - -Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) -Number of replicates: 10000 - - tree li Dli +- SE pKH pSH pRELL - - 1* -904.637 0.000 0.000 -1.000 -1.000 0.511 - 2 -904.637 -0.000 0.000 0.500 0.516 0.489 - -pKH: P value for KH normal test (Kishino & Hasegawa 1989) -pRELL: RELL bootstrap proportions (Kishino & Hasegawa 1989) -pSH: P value with multiple-comparison correction (MC in table 1 of Shimodaira & Hasegawa 1999) -(-1 for P values means N/A) diff --git a/t/data/codeml_lysozyme/rst b/t/data/codeml_lysozyme/rst deleted file mode 100644 index c09f49c4d..000000000 --- a/t/data/codeml_lysozyme/rst +++ /dev/null @@ -1,1165 +0,0 @@ -Supplemental results for CODEML (seqf: lysozymeSmall.txt treef: lysozymeSmall.trees) - -Number of codon sites with 0,1,2,3 position differences - 2 vs. 1 122 8 0 0 0.2782 (0.0133 0.0478) - 3 vs. 1 107 20 2 1 1.1086 (0.0742 0.0670) - 3 vs. 2 108 18 3 1 1.1055 (0.0742 0.0671) - 4 vs. 1 108 18 4 0 1.1979 (0.0725 0.0605) - 4 vs. 2 105 20 5 0 0.9234 (0.0797 0.0863) - 4 vs. 3 118 12 0 0 0.5517 (0.0267 0.0484) - 5 vs. 1 114 13 3 0 1.8744 (0.0562 0.0300) - 5 vs. 2 113 13 4 0 1.0215 (0.0561 0.0550) - 5 vs. 3 115 13 2 0 1.2973 (0.0473 0.0364) - 5 vs. 4 114 14 2 0 1.3970 (0.0508 0.0364) - 6 vs. 1 106 19 5 0 0.4701 (0.0633 0.1346) - 6 vs. 2 107 17 6 0 0.4688 (0.0633 0.1349) - 6 vs. 3 104 20 4 2 0.5159 (0.0775 0.1502) - 6 vs. 4 98 25 6 1 0.5833 (0.0959 0.1645) - 6 vs. 5 110 14 6 0 0.4544 (0.0559 0.1230) - 7 vs. 1 103 25 2 0 0.4725 (0.0634 0.1341) - 7 vs. 2 106 21 3 0 0.5925 (0.0633 0.1069) - 7 vs. 3 105 20 3 2 0.4702 (0.0704 0.1496) - 7 vs. 4 99 25 5 1 0.5411 (0.0886 0.1638) - 7 vs. 5 110 16 4 0 0.3995 (0.0490 0.1225) - 7 vs. 6 122 8 0 0 0.1595 (0.0099 0.0619) - - -TREE # 1 - -Ancestral reconstruction by CODONML. - -((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); - -((1, 2), ((3, 4), 5), (6, 7)); - - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - -tree with node labels for Rod Page's TreeView -((1_Hsa_Human: 0.007565, 2_Hla_gibbon: 0.011517) 9 : 0.020710, ((3_Cgu/Can_colobus: 0.012982, 4_Pne_langur: 0.015429) 11 : 0.032838, 5_Mmu_rhesus: 0.005765) 10 : 0.012982, (6_Ssc_squirrelM: 0.012140, 7_Cja_marmoset: 0.007035) 12 : 0.035889) 8 ; - -Nodes 8 to 12 are ancestral - -(1) Marginal reconstruction of ancestral sequences (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650). - - -Prob of best character at each node, listed by site - -Site Freq Data: - - 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) - 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC V 0.967 (V 0.967) GTC V 1.000 (V 1.000) ATC I 0.992 (I 0.992) ATC I 1.000 (I 1.000) GTC V 1.000 (V 1.000) - 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 0.985 (F 1.000) - 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) - 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) - 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) - 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) - 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) - 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) - 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) - 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA R 0.990 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.998 (R 0.998) AAA K 0.994 (K 0.994) AGG R 0.998 (R 1.000) - 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG L 0.999 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTT F 0.990 (F 0.990) - 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG L 0.871 (L 0.871) ATG M 1.000 (M 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 0.871 (L 0.871) - 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) - 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 0.998 (R 0.998) AAG K 0.995 (K 0.995) AGG R 1.000 (R 1.000) - 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 0.999 (I 0.999) GTC V 0.996 (V 0.996) ATC I 1.000 (I 1.000) - 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) - 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG M 0.974 (M 0.974) ATG M 1.000 (M 1.000) GTG V 0.993 (V 0.993) GTG V 1.000 (V 1.000) ATG M 1.000 (M 1.000) - 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) - 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) - 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) - 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT D 0.742 (D 0.743) GGT G 0.996 (G 0.996) GAT D 0.696 (D 0.696) GGT G 0.993 (G 0.993) GAT D 0.959 (D 0.999) - 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 0.999 (Y 1.000) TAT Y 0.962 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) - 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) - 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA R 0.977 (R 0.978) CGA R 1.000 (R 1.000) CAA Q 0.990 (Q 0.990) GAA E 0.992 (E 0.992) CGT R 1.000 (R 1.000) - 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) - 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) - 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT P 1.000 (P 1.000) CCT P 0.998 (P 0.998) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) - 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 0.989 (D 1.000) GAC D 1.000 (D 1.000) - 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA Q 0.980 (Q 0.980) AGA R 0.994 (R 0.995) CAA Q 0.990 (Q 0.990) GAA E 0.998 (E 0.998) CAA Q 1.000 (Q 1.000) - 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) - 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) - 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) - 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) - 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) - 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) - 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) - 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC H 0.742 (H 0.742) CGC R 0.999 (R 0.999) CAC H 0.748 (H 0.748) CGC R 0.998 (R 0.998) CAC H 1.000 (H 1.000) - 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC Y 0.994 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAT Y 0.997 (Y 1.000) - 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT N 0.998 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.889 (N 1.000) - 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 0.970 (N 0.970) GAT D 0.994 (D 0.994) AAT N 0.999 (N 0.999) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA K 0.992 (K 0.992) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AGA R 0.998 (R 0.998) - 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) - 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) - 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.964 (N 0.964) AAT N 1.000 (N 1.000) - 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) - 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 0.997 (I 0.997) TTA L 1.000 (L 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) - 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) - 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) - 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT N 0.998 (N 0.998) AAT N 0.957 (N 0.957) AAT N 0.999 (N 0.999) AAT N 0.963 (N 0.963) AAT N 1.000 (N 1.000) - 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) - 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 0.996 (D 0.997) AAT N 0.983 (N 0.993) GAT D 1.000 (D 1.000) - 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC N 0.993 (N 0.993) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) GAC D 0.998 (D 0.998) - 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) - 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT A 0.994 (A 0.994) GCT A 0.985 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) ACT T 0.998 (T 0.998) - 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT D 0.997 (D 0.997) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAA E 0.995 (E 0.995) - 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA V 0.993 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTG V 0.998 (V 1.000) - 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT A 0.990 (A 0.998) GCT A 1.000 (A 1.000) GCT A 0.947 (A 0.947) GCT A 1.000 (A 1.000) GCC A 0.998 (A 1.000) - 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) - 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) - 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) - 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT R 0.973 (R 0.993) CGT R 0.970 (R 1.000) AGT S 0.995 (S 0.996) AGT S 1.000 (S 1.000) CGT R 0.935 (R 1.000) - 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) - 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 0.978 (I 0.978) ATT I 1.000 (I 1.000) - 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA R 0.999 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.996 (R 1.000) CGA R 0.996 (R 1.000) AGA R 0.921 (R 1.000) - 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) - 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA R 0.990 (R 0.990) AGA R 1.000 (R 1.000) AGA R 0.997 (R 0.997) AGA R 0.962 (R 0.962) AAA K 0.998 (K 0.998) - 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT N 0.984 (N 0.984) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.987 (N 0.988) GCT A 0.998 (A 0.998) - 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT H 0.952 (H 0.990) CGT R 0.998 (R 0.998) CAC H 0.998 (H 1.000) CAC H 1.000 (H 1.000) CAT H 1.000 (H 1.000) - 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.975 (R 0.975) AGA R 1.000 (R 1.000) - 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 0.998 (V 0.998) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) - 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 0.993 (S 0.993) CGT R 0.999 (R 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) - 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) - 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 0.993 (Y 1.000) TAT Y 1.000 (Y 1.000) - 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 0.988 (V 0.988) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) GAA E 0.517 (E 0.517) CAA Q 1.000 (Q 1.000) - 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) - 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG V 0.797 (V 1.000) GTG V 0.795 (V 1.000) GTG V 0.942 (V 1.000) GTG V 0.937 (V 1.000) GTA V 0.998 (V 1.000) - -Summary of changes along branches. -Check root for directions of change. - -Branch 1: 8..9 (n= 8.5 s= 0.5) - - 17 L 0.871 -> M 1.000 - 37 D 0.743 -> G 0.996 - 50 Q 0.980 -> R 0.995 - 62 H 0.742 -> R 0.999 - 67 N 0.970 -> D 0.994 - 79 I 0.997 -> L 1.000 - 115 H 0.990 -> R 0.998 - 122 S 0.993 -> R 1.000 - - -Branch 2: 9..1 (Hsa_Human) (n= 2.0 s= 1.0) - - 47 P 0.998 -> A - 82 N 0.957 -> S - - -Branch 3: 9..2 (Hla_gibbon) (n= 2.0 s= 3.0) - - 121 V 0.998 -> L - 125 V 0.988 -> I - - -Branch 4: 8..10 (n= 4.0 s= 1.0) - - 2 V 0.967 -> I 0.992 - 29 M 0.974 -> V 0.993 - 41 R 0.978 -> Q 0.990 - 101 R 0.993 -> S 0.996 - - -Branch 5: 10..11 (n= 9.0 s= 1.0) - - 14 R 0.998 -> K 0.994 - 21 R 0.998 -> K 0.995 - 23 I 0.999 -> V 0.996 - 37 D 0.696 -> G 0.993 - 41 Q 0.990 -> E 0.992 - 50 Q 0.990 -> E 0.998 - 62 H 0.748 -> R 0.998 - 87 D 0.997 -> N 0.993 - 126 Q 1.000 -> E 0.517 - - -Branch 6: 11..3 (Cgu/Can_colobus) (n= 3.0 s= 2.0) - - 41 E 0.992 -> D - 113 R 0.962 -> K - 114 N 0.988 -> K - - -Branch 7: 11..4 (Pne_langur) (n= 5.0 s= 2.0) - - 75 N 0.964 -> D - 82 N 0.963 -> S - 106 I 0.978 -> V - 119 R 0.975 -> K - 126 E 0.517 -> K - - -Branch 8: 10..5 (Mmu_rhesus) (n= 2.0 s= 0.0) - - 37 D 0.696 -> N - 94 A 0.947 -> T - - -Branch 9: 8..12 (n= 8.0 s= 6.0) - - 15 L 1.000 -> F 0.990 - 69 K 0.992 -> R 0.998 - 88 N 0.993 -> D 0.998 - 90 A 0.994 -> T 0.998 - 91 D 0.997 -> E 0.995 - 113 R 0.990 -> K 0.998 - 114 N 0.984 -> A 0.998 - - -Branch 10: 12..6 (Ssc_squirrelM) (n= 3.0 s= 2.0) - - 15 F 0.990 -> L - 17 L 0.871 -> M - 91 E 0.995 -> Q - - -Branch 11: 12..7 (Cja_marmoset) (n= 0.0 s= 3.0) - - - - - -List of extant and reconstructed sequences - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG -node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - -Overall accuracy of the 5 ancestral sequences: - 0.99108 0.99716 0.99439 0.99393 0.99633 -for a site. - - 0.27875 0.67341 0.43633 0.37872 0.60699 -for the sequence. - - -Amino acid sequences inferred by codonml. - -Node #8 KVFERCELAR TLKRLGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNHCQNRD VSQYVQGCGV -Node #9 KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNPGDR STDYGIFQIN SRYWCNDGKT PGAVNACHLS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNRCQNRD VRQYVQGCGV -Node #10 KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVQGCGV -Node #11 KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE STDYGIFQIN SRYWCNNGKT PGAVNACHIS CNALLQNNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVEGCGV -Node #12 KVFERCELAR TLKRFGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGRT PGAVNACHIS CNALLQDDIT EAVACAKRVV RDPQGIRAWV AWKAHCQNRD VSQYVQGCGV - - -Changes at sites (syn nonsyn). - - 1 (0.0 0.0) - 2 GTC.ATC (0.0 1.0) - 3 TTT.TTC (1.0 0.0) - 4 (0.0 0.0) - 5 (0.0 0.0) - 6 (0.0 0.0) - 7 (0.0 0.0) - 8 (0.0 0.0) - 9 (0.0 0.0) - 10 (0.0 0.0) - 11 (0.0 0.0) - 12 (0.0 0.0) - 13 (0.0 0.0) - 14 AGA.AAA AGA.AGG (1.0 1.0) - 15 TTT.CTT TTG.TTT (0.0 2.0) - 16 (0.0 0.0) - 17 CTG.ATG CTG.ATG (0.0 2.0) - 18 (0.0 0.0) - 19 (0.0 0.0) - 20 (0.0 0.0) - 21 AGG.AAG (0.0 1.0) - 22 (0.0 0.0) - 23 ATC.GTC (0.0 1.0) - 24 (0.0 0.0) - 25 (0.0 0.0) - 26 (0.0 0.0) - 27 (0.0 0.0) - 28 (0.0 0.0) - 29 ATG.GTG (0.0 1.0) - 30 (0.0 0.0) - 31 (0.0 0.0) - 32 (0.0 0.0) - 33 (0.0 0.0) - 34 (0.0 0.0) - 35 (0.0 0.0) - 36 (0.0 0.0) - 37 GAT.AAT GAT.GAC GAT.GGT GAT.GGT (1.0 3.0) - 38 TAT.TAC (1.0 0.0) - 39 (0.0 0.0) - 40 (0.0 0.0) - 41 GAA.GAC CGA.CAA CAA.GAA CGA.CGT (1.0 3.0) - 42 (0.0 0.0) - 43 (0.0 0.0) - 44 (0.0 0.0) - 45 (0.0 0.0) - 46 (0.0 0.0) - 47 CCT.GCT (0.0 1.0) - 48 (0.0 0.0) - 49 GAC.GAT (1.0 0.0) - 50 CAA.AGA CAA.GAA (0.5 2.5) - 51 (0.0 0.0) - 52 (0.0 0.0) - 53 (0.0 0.0) - 54 (0.0 0.0) - 55 (0.0 0.0) - 56 (0.0 0.0) - 57 (0.0 0.0) - 58 (0.0 0.0) - 59 (0.0 0.0) - 60 (0.0 0.0) - 61 (0.0 0.0) - 62 CAC.CGC CAC.CGC (0.0 2.0) - 63 TAC.TAT (1.0 0.0) - 64 (0.0 0.0) - 65 (0.0 0.0) - 66 AAT.AAC (1.0 0.0) - 67 AAT.GAT (0.0 1.0) - 68 (0.0 0.0) - 69 AAA.AGA (0.0 1.0) - 70 (0.0 0.0) - 71 (0.0 0.0) - 72 (0.0 0.0) - 73 (0.0 0.0) - 74 (0.0 0.0) - 75 AAT.GAT (0.0 1.0) - 76 (0.0 0.0) - 77 (0.0 0.0) - 78 (0.0 0.0) - 79 ATA.TTA (0.0 1.0) - 80 (0.0 0.0) - 81 (0.0 0.0) - 82 AAT.AGT AAT.AGT (0.0 2.0) - 83 (0.0 0.0) - 84 (0.0 0.0) - 85 (0.0 0.0) - 86 (0.0 0.0) - 87 AAT.AAC GAT.AAT (1.0 1.0) - 88 AAC.GAC (0.0 1.0) - 89 (0.0 0.0) - 90 GCT.GCC GCT.ACT (1.0 1.0) - 91 GAA.CAA GAT.GAA (0.0 2.0) - 92 (0.0 0.0) - 93 GTA.GTG (1.0 0.0) - 94 GCT.ACT GCT.GCC (1.0 1.0) - 95 (0.0 0.0) - 96 (0.0 0.0) - 97 (0.0 0.0) - 98 (0.0 0.0) - 99 (0.0 0.0) - 100 (0.0 0.0) - 101 CGT.CGC CGT.CGC CGT.AGT (2.0 1.0) - 102 (0.0 0.0) - 103 (0.0 0.0) - 104 (0.0 0.0) - 105 (0.0 0.0) - 106 ATT.GTT (0.0 1.0) - 107 AGA.AGG AGA.CGA (2.0 0.0) - 108 (0.0 0.0) - 109 (0.0 0.0) - 110 (0.0 0.0) - 111 (0.0 0.0) - 112 (0.0 0.0) - 113 AGA.AAA AGA.AAA (0.0 2.0) - 114 AAT.AAG AAT.GCT (0.0 3.0) - 115 CAT.CGT CAT.CAC (1.0 1.0) - 116 (0.0 0.0) - 117 (0.0 0.0) - 118 (0.0 0.0) - 119 AGA.AAA (0.0 1.0) - 120 (0.0 0.0) - 121 GTC.CTC (0.0 1.0) - 122 AGT.CGT (0.0 1.0) - 123 (0.0 0.0) - 124 TAT.TAC (1.0 0.0) - 125 GTT.ATT (0.0 1.0) - 126 GAA.AAA CAA.GAA (0.0 2.0) - 127 (0.0 0.0) - 128 (0.0 0.0) - 129 (0.0 0.0) - 130 GTG.GTA GTG.GTA GTG.GTA (3.0 0.0) - - -(2) Joint reconstruction of ancestral sequences (eqn. 2 in Yang et al. 1995 Genetics 141:1641-1650), using the algorithm of Pupko et al. (2000 Mol Biol Evol 17:890-896). - -Listed by site, reconstruction (prob.) - - -Site Freq Data: - - 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) - 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC GTC ATC ATC GTC (0.9589) - 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT TTT TTT TTT TTT (0.9846) - 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA GAA GAA GAA GAA (0.9999) - 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) - 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) - 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9999) - 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) - 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) - 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) - 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA AGA AGA AAA AGG (0.9789) - 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG TTG TTG TTG TTT (0.9894) - 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG ATG CTG CTG CTG (0.8701) - 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) - 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AAG AGG (0.9935) - 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC ATC ATC GTC ATC (0.9950) - 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA CTA CTA CTA CTA (1.0000) - 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG ATG GTG GTG ATG (0.9668) - 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) - 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) - 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT AGT AGT AGT AGT (0.9998) - 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT GGT GAT GGT GAT (0.6376) - 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9616) - 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) - 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA CGA CAA GAA CGT (0.9586) - 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) - 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) - 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) - 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT CCT CCT CCT CCT (0.9979) - 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC GAC GAC GAC GAC (0.9890) - 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA AGA CAA GAA CAA (0.9726) - 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) - 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (1.0000) - 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG GGG GGG GGG GGG (1.0000) - 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA ATA ATA ATA ATA (1.0000) - 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT TTT TTT TTT TTT (1.0000) - 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) - 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) - 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) - 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC CGC CAC CGC CAC (0.7383) - 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC TAC TAC TAC TAT (0.9908) - 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT AAT AAT AAT AAT (0.8888) - 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT GAT AAT AAT AAT (0.9642) - 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA AAA AAA AAA AGA (0.9899) - 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC ACC ACC ACC ACC (1.0000) - 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) - 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) - 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9638) - 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT CAT CAT CAT CAT (1.0000) - 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA TTA ATA ATA ATA (0.9961) - 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC TCC TCC TCC TCC (1.0000) - 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC TGC TGC TGC TGC (1.0000) - 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9225) - 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) - 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT GAT GAT AAT GAT (0.9799) - 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC AAC AAC AAC GAC (0.9905) - 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) - 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT GCT GCT GCT ACT (0.9782) - 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT GAT GAT GAT GAA (0.9916) - 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA GTA GTA GTA GTG (0.9911) - 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT GCT GCT GCT GCC (0.9373) - 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) - 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) - 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) - 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (1.0000) - 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT CGT AGT AGT CGT (0.9153) - 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) - 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT ATT ATT ATT ATT (0.9779) - 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA AGA AGA CGA AGA (0.9144) - 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG GTG GTG GTG GTG (1.0000) - 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA AGA AGA AGA AAA (0.9527) - 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT AAT AAT AAT GCT (0.9702) - 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT CGT CAC CAC CAT (0.9482) - 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9748) - 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (0.9981) - 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT CGT AGT AGT AGT (0.9920) - 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) - 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9932) - 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9882) - 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA GAA CAA (0.5165) - 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT GGT GGT GGT GGT (0.9998) - 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG GTG GTG GTG GTA (0.7827) - - -List of extant and reconstructed sequences - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG -node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - - -TREE # 2 - -Ancestral reconstruction by CODONML. - -((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005766): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889); - -((1, 2), ((3, 4), 5), (6, 7)); - - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - -tree with node labels for Rod Page's TreeView -((1_Hsa_Human: 0.007565, 2_Hla_gibbon: 0.011517) 9 : 0.020710, ((3_Cgu/Can_colobus: 0.012982, 4_Pne_langur: 0.015429) 11 : 0.032838, 5_Mmu_rhesus: 0.005766) 10 : 0.012982, (6_Ssc_squirrelM: 0.012140, 7_Cja_marmoset: 0.007035) 12 : 0.035889) 8 ; - -Nodes 8 to 12 are ancestral - -(1) Marginal reconstruction of ancestral sequences (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650). - - -Prob of best character at each node, listed by site - -Site Freq Data: - - 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) - 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC V 0.967 (V 0.967) GTC V 1.000 (V 1.000) ATC I 0.992 (I 0.992) ATC I 1.000 (I 1.000) GTC V 1.000 (V 1.000) - 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 0.985 (F 1.000) - 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) GAA E 1.000 (E 1.000) - 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) - 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) - 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) - 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) - 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) - 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) - 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA R 0.990 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.998 (R 0.998) AAA K 0.994 (K 0.994) AGG R 0.998 (R 1.000) - 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG L 0.999 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTT F 0.990 (F 0.990) - 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG L 0.871 (L 0.871) ATG M 1.000 (M 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 0.871 (L 0.871) - 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) - 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 0.998 (R 0.998) AAG K 0.995 (K 0.995) AGG R 1.000 (R 1.000) - 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 0.999 (I 0.999) GTC V 0.996 (V 0.996) ATC I 1.000 (I 1.000) - 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) CTA L 1.000 (L 1.000) - 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG M 0.974 (M 0.974) ATG M 1.000 (M 1.000) GTG V 0.993 (V 0.993) GTG V 1.000 (V 1.000) ATG M 1.000 (M 1.000) - 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) - 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) GAG E 1.000 (E 1.000) - 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) - 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT D 0.742 (D 0.743) GGT G 0.996 (G 0.996) GAT D 0.696 (D 0.696) GGT G 0.993 (G 0.993) GAT D 0.959 (D 0.999) - 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 0.999 (Y 1.000) TAT Y 0.962 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) - 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) - 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA R 0.977 (R 0.978) CGA R 1.000 (R 1.000) CAA Q 0.990 (Q 0.990) GAA E 0.992 (E 0.992) CGT R 1.000 (R 1.000) - 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) ACA T 1.000 (T 1.000) - 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) - 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT P 1.000 (P 1.000) CCT P 0.998 (P 0.998) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) CCT P 1.000 (P 1.000) - 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 1.000 (D 1.000) GAC D 0.989 (D 1.000) GAC D 1.000 (D 1.000) - 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA Q 0.980 (Q 0.980) AGA R 0.994 (R 0.995) CAA Q 0.990 (Q 0.990) GAA E 0.998 (E 0.998) CAA Q 1.000 (Q 1.000) - 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) ACT T 1.000 (T 1.000) - 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) - 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) GGG G 1.000 (G 1.000) - 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) - 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) TTT F 1.000 (F 1.000) - 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) - 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) - 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) AGC S 1.000 (S 1.000) - 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC H 0.742 (H 0.742) CGC R 0.999 (R 0.999) CAC H 0.748 (H 0.748) CGC R 0.998 (R 0.998) CAC H 1.000 (H 1.000) - 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC Y 0.994 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAC Y 1.000 (Y 1.000) TAT Y 0.997 (Y 1.000) - 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT N 0.998 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.889 (N 1.000) - 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT N 0.970 (N 0.970) GAT D 0.994 (D 0.994) AAT N 0.999 (N 0.999) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) - 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA K 0.992 (K 0.992) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AAA K 1.000 (K 1.000) AGA R 0.998 (R 0.998) - 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) ACC T 1.000 (T 1.000) - 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) - 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.964 (N 0.964) AAT N 1.000 (N 1.000) - 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) GCC A 1.000 (A 1.000) - 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) CAT H 1.000 (H 1.000) - 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA I 0.997 (I 0.997) TTA L 1.000 (L 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) ATA I 1.000 (I 1.000) - 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) TCC S 1.000 (S 1.000) - 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) TGC C 1.000 (C 1.000) - 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT N 0.998 (N 0.998) AAT N 0.957 (N 0.957) AAT N 0.999 (N 0.999) AAT N 0.963 (N 0.963) AAT N 1.000 (N 1.000) - 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) TTG L 1.000 (L 1.000) - 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) CTG L 1.000 (L 1.000) - 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 0.996 (D 0.997) AAT N 0.983 (N 0.993) GAT D 1.000 (D 1.000) - 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC N 0.993 (N 0.993) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) GAC D 0.998 (D 0.998) - 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) ATC I 1.000 (I 1.000) - 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT A 0.994 (A 0.994) GCT A 0.985 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) ACT T 0.998 (T 0.998) - 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT D 0.997 (D 0.997) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAA E 0.995 (E 0.995) - 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) GCT A 1.000 (A 1.000) - 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA V 0.993 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTA V 1.000 (V 1.000) GTG V 0.998 (V 1.000) - 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT A 0.990 (A 0.998) GCT A 1.000 (A 1.000) GCT A 0.947 (A 0.947) GCT A 1.000 (A 1.000) GCC A 0.998 (A 1.000) - 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) AAG K 1.000 (K 1.000) - 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) AGG R 1.000 (R 1.000) - 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) - 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT R 0.973 (R 0.993) CGT R 0.970 (R 1.000) AGT S 0.995 (S 0.996) AGT S 1.000 (S 1.000) CGT R 0.935 (R 1.000) - 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) CCA P 1.000 (P 1.000) - 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) GGC G 1.000 (G 1.000) - 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 1.000 (I 1.000) ATT I 0.978 (I 0.978) ATT I 1.000 (I 1.000) - 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA R 0.999 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.996 (R 1.000) CGA R 0.996 (R 1.000) AGA R 0.921 (R 1.000) - 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) GTG V 1.000 (V 1.000) - 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) GCA A 1.000 (A 1.000) - 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) TGG W 1.000 (W 1.000) - 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA R 0.990 (R 0.990) AGA R 1.000 (R 1.000) AGA R 0.997 (R 0.997) AGA R 0.962 (R 0.962) AAA K 0.998 (K 0.998) - 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT N 0.984 (N 0.984) AAT N 1.000 (N 1.000) AAT N 1.000 (N 1.000) AAT N 0.987 (N 0.988) GCT A 0.998 (A 0.998) - 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT H 0.952 (H 0.990) CGT R 0.998 (R 0.998) CAC H 0.998 (H 1.000) CAC H 1.000 (H 1.000) CAT H 1.000 (H 1.000) - 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) - 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) AAC N 1.000 (N 1.000) - 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 1.000 (R 1.000) AGA R 0.975 (R 0.975) AGA R 1.000 (R 1.000) - 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) GAT D 1.000 (D 1.000) - 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC V 1.000 (V 1.000) GTC V 0.998 (V 0.998) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) GTC V 1.000 (V 1.000) - 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT S 0.993 (S 0.993) CGT R 0.999 (R 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) AGT S 1.000 (S 1.000) - 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) CAG Q 1.000 (Q 1.000) - 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 1.000 (Y 1.000) TAT Y 0.993 (Y 1.000) TAT Y 1.000 (Y 1.000) - 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT V 1.000 (V 1.000) GTT V 0.988 (V 0.988) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) GTT V 1.000 (V 1.000) - 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) CAA Q 1.000 (Q 1.000) GAA E 0.517 (E 0.517) CAA Q 1.000 (Q 1.000) - 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) GGT G 1.000 (G 1.000) - 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) TGT C 1.000 (C 1.000) - 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) GGA G 1.000 (G 1.000) - 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG V 0.797 (V 1.000) GTG V 0.795 (V 1.000) GTG V 0.942 (V 1.000) GTG V 0.937 (V 1.000) GTA V 0.998 (V 1.000) - -Summary of changes along branches. -Check root for directions of change. - -Branch 1: 8..9 (n= 8.5 s= 0.5) - - 17 L 0.871 -> M 1.000 - 37 D 0.743 -> G 0.996 - 50 Q 0.980 -> R 0.995 - 62 H 0.742 -> R 0.999 - 67 N 0.970 -> D 0.994 - 79 I 0.997 -> L 1.000 - 115 H 0.990 -> R 0.998 - 122 S 0.993 -> R 1.000 - - -Branch 2: 9..1 (Hsa_Human) (n= 2.0 s= 1.0) - - 47 P 0.998 -> A - 82 N 0.957 -> S - - -Branch 3: 9..2 (Hla_gibbon) (n= 2.0 s= 3.0) - - 121 V 0.998 -> L - 125 V 0.988 -> I - - -Branch 4: 8..10 (n= 4.0 s= 1.0) - - 2 V 0.967 -> I 0.992 - 29 M 0.974 -> V 0.993 - 41 R 0.978 -> Q 0.990 - 101 R 0.993 -> S 0.996 - - -Branch 5: 10..11 (n= 9.0 s= 1.0) - - 14 R 0.998 -> K 0.994 - 21 R 0.998 -> K 0.995 - 23 I 0.999 -> V 0.996 - 37 D 0.696 -> G 0.993 - 41 Q 0.990 -> E 0.992 - 50 Q 0.990 -> E 0.998 - 62 H 0.748 -> R 0.998 - 87 D 0.997 -> N 0.993 - 126 Q 1.000 -> E 0.517 - - -Branch 6: 11..3 (Cgu/Can_colobus) (n= 3.0 s= 2.0) - - 41 E 0.992 -> D - 113 R 0.962 -> K - 114 N 0.988 -> K - - -Branch 7: 11..4 (Pne_langur) (n= 5.0 s= 2.0) - - 75 N 0.964 -> D - 82 N 0.963 -> S - 106 I 0.978 -> V - 119 R 0.975 -> K - 126 E 0.517 -> K - - -Branch 8: 10..5 (Mmu_rhesus) (n= 2.0 s= 0.0) - - 37 D 0.696 -> N - 94 A 0.947 -> T - - -Branch 9: 8..12 (n= 8.0 s= 6.0) - - 15 L 1.000 -> F 0.990 - 69 K 0.992 -> R 0.998 - 88 N 0.993 -> D 0.998 - 90 A 0.994 -> T 0.998 - 91 D 0.997 -> E 0.995 - 113 R 0.990 -> K 0.998 - 114 N 0.984 -> A 0.998 - - -Branch 10: 12..6 (Ssc_squirrelM) (n= 3.0 s= 2.0) - - 15 F 0.990 -> L - 17 L 0.871 -> M - 91 E 0.995 -> Q - - -Branch 11: 12..7 (Cja_marmoset) (n= 0.0 s= 3.0) - - - - - -List of extant and reconstructed sequences - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG -node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - -Overall accuracy of the 5 ancestral sequences: - 0.99108 0.99716 0.99439 0.99393 0.99633 -for a site. - - 0.27875 0.67341 0.43633 0.37872 0.60699 -for the sequence. - - -Amino acid sequences inferred by codonml. - -Node #8 KVFERCELAR TLKRLGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNHCQNRD VSQYVQGCGV -Node #9 KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNPGDR STDYGIFQIN SRYWCNDGKT PGAVNACHLS CNALLQDNIA DAVACAKRVV RDPQGIRAWV AWRNRCQNRD VRQYVQGCGV -Node #10 KIFERCELAR TLKRLGLDGY RGISLANWVC LAKWESDYNT QATNYNPGDQ STDYGIFQIN SHYWCNNGKT PGAVNACHIS CNALLQDNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVQGCGV -Node #11 KIFERCELAR TLKKLGLDGY KGVSLANWVC LAKWESGYNT EATNYNPGDE STDYGIFQIN SRYWCNNGKT PGAVNACHIS CNALLQNNIA DAVACAKRVV SDPQGIRAWV AWRNHCQNRD VSQYVEGCGV -Node #12 KVFERCELAR TLKRFGLDGY RGISLANWMC LAKWESDYNT RATNYNPGDQ STDYGIFQIN SHYWCNNGRT PGAVNACHIS CNALLQDDIT EAVACAKRVV RDPQGIRAWV AWKAHCQNRD VSQYVQGCGV - - -Changes at sites (syn nonsyn). - - 1 (0.0 0.0) - 2 GTC.ATC (0.0 1.0) - 3 TTT.TTC (1.0 0.0) - 4 (0.0 0.0) - 5 (0.0 0.0) - 6 (0.0 0.0) - 7 (0.0 0.0) - 8 (0.0 0.0) - 9 (0.0 0.0) - 10 (0.0 0.0) - 11 (0.0 0.0) - 12 (0.0 0.0) - 13 (0.0 0.0) - 14 AGA.AAA AGA.AGG (1.0 1.0) - 15 TTT.CTT TTG.TTT (0.0 2.0) - 16 (0.0 0.0) - 17 CTG.ATG CTG.ATG (0.0 2.0) - 18 (0.0 0.0) - 19 (0.0 0.0) - 20 (0.0 0.0) - 21 AGG.AAG (0.0 1.0) - 22 (0.0 0.0) - 23 ATC.GTC (0.0 1.0) - 24 (0.0 0.0) - 25 (0.0 0.0) - 26 (0.0 0.0) - 27 (0.0 0.0) - 28 (0.0 0.0) - 29 ATG.GTG (0.0 1.0) - 30 (0.0 0.0) - 31 (0.0 0.0) - 32 (0.0 0.0) - 33 (0.0 0.0) - 34 (0.0 0.0) - 35 (0.0 0.0) - 36 (0.0 0.0) - 37 GAT.AAT GAT.GAC GAT.GGT GAT.GGT (1.0 3.0) - 38 TAT.TAC (1.0 0.0) - 39 (0.0 0.0) - 40 (0.0 0.0) - 41 GAA.GAC CGA.CAA CAA.GAA CGA.CGT (1.0 3.0) - 42 (0.0 0.0) - 43 (0.0 0.0) - 44 (0.0 0.0) - 45 (0.0 0.0) - 46 (0.0 0.0) - 47 CCT.GCT (0.0 1.0) - 48 (0.0 0.0) - 49 GAC.GAT (1.0 0.0) - 50 CAA.AGA CAA.GAA (0.5 2.5) - 51 (0.0 0.0) - 52 (0.0 0.0) - 53 (0.0 0.0) - 54 (0.0 0.0) - 55 (0.0 0.0) - 56 (0.0 0.0) - 57 (0.0 0.0) - 58 (0.0 0.0) - 59 (0.0 0.0) - 60 (0.0 0.0) - 61 (0.0 0.0) - 62 CAC.CGC CAC.CGC (0.0 2.0) - 63 TAC.TAT (1.0 0.0) - 64 (0.0 0.0) - 65 (0.0 0.0) - 66 AAT.AAC (1.0 0.0) - 67 AAT.GAT (0.0 1.0) - 68 (0.0 0.0) - 69 AAA.AGA (0.0 1.0) - 70 (0.0 0.0) - 71 (0.0 0.0) - 72 (0.0 0.0) - 73 (0.0 0.0) - 74 (0.0 0.0) - 75 AAT.GAT (0.0 1.0) - 76 (0.0 0.0) - 77 (0.0 0.0) - 78 (0.0 0.0) - 79 ATA.TTA (0.0 1.0) - 80 (0.0 0.0) - 81 (0.0 0.0) - 82 AAT.AGT AAT.AGT (0.0 2.0) - 83 (0.0 0.0) - 84 (0.0 0.0) - 85 (0.0 0.0) - 86 (0.0 0.0) - 87 AAT.AAC GAT.AAT (1.0 1.0) - 88 AAC.GAC (0.0 1.0) - 89 (0.0 0.0) - 90 GCT.GCC GCT.ACT (1.0 1.0) - 91 GAA.CAA GAT.GAA (0.0 2.0) - 92 (0.0 0.0) - 93 GTA.GTG (1.0 0.0) - 94 GCT.ACT GCT.GCC (1.0 1.0) - 95 (0.0 0.0) - 96 (0.0 0.0) - 97 (0.0 0.0) - 98 (0.0 0.0) - 99 (0.0 0.0) - 100 (0.0 0.0) - 101 CGT.CGC CGT.CGC CGT.AGT (2.0 1.0) - 102 (0.0 0.0) - 103 (0.0 0.0) - 104 (0.0 0.0) - 105 (0.0 0.0) - 106 ATT.GTT (0.0 1.0) - 107 AGA.AGG AGA.CGA (2.0 0.0) - 108 (0.0 0.0) - 109 (0.0 0.0) - 110 (0.0 0.0) - 111 (0.0 0.0) - 112 (0.0 0.0) - 113 AGA.AAA AGA.AAA (0.0 2.0) - 114 AAT.AAG AAT.GCT (0.0 3.0) - 115 CAT.CGT CAT.CAC (1.0 1.0) - 116 (0.0 0.0) - 117 (0.0 0.0) - 118 (0.0 0.0) - 119 AGA.AAA (0.0 1.0) - 120 (0.0 0.0) - 121 GTC.CTC (0.0 1.0) - 122 AGT.CGT (0.0 1.0) - 123 (0.0 0.0) - 124 TAT.TAC (1.0 0.0) - 125 GTT.ATT (0.0 1.0) - 126 GAA.AAA CAA.GAA (0.0 2.0) - 127 (0.0 0.0) - 128 (0.0 0.0) - 129 (0.0 0.0) - 130 GTG.GTA GTG.GTA GTG.GTA (3.0 0.0) - - -(2) Joint reconstruction of ancestral sequences (eqn. 2 in Yang et al. 1995 Genetics 141:1641-1650), using the algorithm of Pupko et al. (2000 Mol Biol Evol 17:890-896). - -Listed by site, reconstruction (prob.) - - -Site Freq Data: - - 1 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) - 2 1 GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) GTC (V) GTC (V) : GTC GTC ATC ATC GTC (0.9589) - 3 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTC (F) TTT (F) : TTT TTT TTT TTT TTT (0.9846) - 4 1 GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) GAA (E) : GAA GAA GAA GAA GAA (0.9999) - 5 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) - 6 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 7 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) - 8 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 9 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 10 1 AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9999) - 11 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) - 12 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) - 13 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) - 14 1 AGA (R) AGA (R) AAA (K) AAA (K) AGA (R) AGG (R) AGG (R) : AGA AGA AGA AAA AGG (0.9789) - 15 1 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) CTT (L) TTT (F) : TTG TTG TTG TTG TTT (0.9894) - 16 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 17 1 ATG (M) ATG (M) CTG (L) CTG (L) CTG (L) ATG (M) CTG (L) : CTG ATG CTG CTG CTG (0.8701) - 18 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 19 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 20 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) - 21 1 AGG (R) AGG (R) AAG (K) AAG (K) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AAG AGG (0.9935) - 22 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 23 1 ATC (I) ATC (I) GTC (V) GTC (V) ATC (I) ATC (I) ATC (I) : ATC ATC ATC GTC ATC (0.9950) - 24 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 25 1 CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) CTA (L) : CTA CTA CTA CTA CTA (1.0000) - 26 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 27 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 28 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 29 1 ATG (M) ATG (M) GTG (V) GTG (V) GTG (V) ATG (M) ATG (M) : ATG ATG GTG GTG ATG (0.9668) - 30 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 31 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 32 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 33 2 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) : AAA AAA AAA AAA AAA (0.9999) - 34 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 35 2 GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) GAG (E) : GAG GAG GAG GAG GAG (0.9999) - 36 1 AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT AGT AGT AGT AGT (0.9998) - 37 1 GGT (G) GGT (G) GGT (G) GGT (G) AAT (N) GAC (D) GAT (D) : GAT GGT GAT GGT GAT (0.6376) - 38 1 TAC (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9616) - 39 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 40 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) - 41 1 CGA (R) CGA (R) GAC (D) GAA (E) CAA (Q) CGT (R) CGT (R) : CGA CGA CAA GAA CGT (0.9586) - 42 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 43 2 ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) ACA (T) : ACA ACA ACA ACA ACA (1.0000) - 44 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 45 2 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) : TAC TAC TAC TAC TAC (1.0000) - 46 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) - 47 1 GCT (A) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) CCT (P) : CCT CCT CCT CCT CCT (0.9979) - 48 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 49 1 GAC (D) GAC (D) GAT (D) GAC (D) GAC (D) GAC (D) GAC (D) : GAC GAC GAC GAC GAC (0.9890) - 50 1 AGA (R) AGA (R) GAA (E) GAA (E) CAA (Q) CAA (Q) CAA (Q) : CAA AGA CAA GAA CAA (0.9726) - 51 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 52 2 ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) ACT (T) : ACT ACT ACT ACT ACT (1.0000) - 53 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 54 1 TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (1.0000) - 55 1 GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) GGG (G) : GGG GGG GGG GGG GGG (1.0000) - 56 1 ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA ATA ATA ATA ATA (1.0000) - 57 1 TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) TTT (F) : TTT TTT TTT TTT TTT (1.0000) - 58 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) - 59 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) - 60 2 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9998) - 61 3 AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) AGC (S) : AGC AGC AGC AGC AGC (0.9999) - 62 1 CGC (R) CGC (R) CGC (R) CGC (R) CAC (H) CAC (H) CAC (H) : CAC CGC CAC CGC CAC (0.7383) - 63 1 TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAC (Y) TAT (Y) TAT (Y) : TAC TAC TAC TAC TAT (0.9908) - 64 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 65 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 66 1 AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) AAC (N) : AAT AAT AAT AAT AAT (0.8888) - 67 1 GAT (D) GAT (D) AAT (N) AAT (N) AAT (N) AAT (N) AAT (N) : AAT GAT AAT AAT AAT (0.9642) - 68 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 69 1 AAA (K) AAA (K) AAA (K) AAA (K) AAA (K) AGA (R) AGA (R) : AAA AAA AAA AAA AGA (0.9899) - 70 1 ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) ACC (T) : ACC ACC ACC ACC ACC (1.0000) - 71 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) - 72 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 73 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 74 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) - 75 1 AAT (N) AAT (N) AAT (N) GAT (D) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9638) - 76 3 GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) GCC (A) : GCC GCC GCC GCC GCC (1.0000) - 77 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 78 1 CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) CAT (H) : CAT CAT CAT CAT CAT (1.0000) - 79 1 TTA (L) TTA (L) ATA (I) ATA (I) ATA (I) ATA (I) ATA (I) : ATA TTA ATA ATA ATA (0.9961) - 80 1 TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) TCC (S) : TCC TCC TCC TCC TCC (1.0000) - 81 1 TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) TGC (C) : TGC TGC TGC TGC TGC (1.0000) - 82 1 AGT (S) AAT (N) AAT (N) AGT (S) AAT (N) AAT (N) AAT (N) : AAT AAT AAT AAT AAT (0.9224) - 83 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 84 3 TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) TTG (L) : TTG TTG TTG TTG TTG (1.0000) - 85 2 CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) CTG (L) : CTG CTG CTG CTG CTG (1.0000) - 86 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 87 1 GAT (D) GAT (D) AAT (N) AAC (N) GAT (D) GAT (D) GAT (D) : GAT GAT GAT AAT GAT (0.9799) - 88 1 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) GAC (D) GAC (D) : AAC AAC AAC AAC GAC (0.9905) - 89 2 ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) ATC (I) : ATC ATC ATC ATC ATC (1.0000) - 90 1 GCT (A) GCC (A) GCT (A) GCT (A) GCT (A) ACT (T) ACT (T) : GCT GCT GCT GCT ACT (0.9782) - 91 1 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) CAA (Q) GAA (E) : GAT GAT GAT GAT GAA (0.9916) - 92 3 GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) GCT (A) : GCT GCT GCT GCT GCT (1.0000) - 93 1 GTA (V) GTA (V) GTA (V) GTA (V) GTA (V) GTG (V) GTG (V) : GTA GTA GTA GTA GTG (0.9911) - 94 1 GCT (A) GCT (A) GCT (A) GCT (A) ACT (T) GCC (A) GCC (A) : GCT GCT GCT GCT GCC (0.9373) - 95 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 96 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 97 2 AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) AAG (K) : AAG AAG AAG AAG AAG (0.9999) - 98 2 AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) AGG (R) : AGG AGG AGG AGG AGG (1.0000) - 99 2 GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9999) - 100 1 GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (1.0000) - 101 1 CGT (R) CGC (R) AGT (S) AGT (S) AGT (S) CGT (R) CGC (R) : CGT CGT AGT AGT CGT (0.9153) - 102 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 103 2 CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) CCA (P) : CCA CCA CCA CCA CCA (1.0000) - 104 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 105 3 GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) GGC (G) : GGC GGC GGC GGC GGC (0.9999) - 106 1 ATT (I) ATT (I) ATT (I) GTT (V) ATT (I) ATT (I) ATT (I) : ATT ATT ATT ATT ATT (0.9779) - 107 1 AGA (R) AGA (R) CGA (R) CGA (R) AGA (R) AGA (R) AGG (R) : AGA AGA AGA CGA AGA (0.9144) - 108 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 109 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 110 1 GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) GTG (V) : GTG GTG GTG GTG GTG (1.0000) - 111 5 GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) GCA (A) : GCA GCA GCA GCA GCA (1.0000) - 112 5 TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) TGG (W) : TGG TGG TGG TGG TGG (1.0000) - 113 1 AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AAA (K) AAA (K) : AGA AGA AGA AGA AAA (0.9527) - 114 1 AAT (N) AAT (N) AAG (K) AAT (N) AAT (N) GCT (A) GCT (A) : AAT AAT AAT AAT GCT (0.9702) - 115 1 CGT (R) CGT (R) CAC (H) CAC (H) CAC (H) CAT (H) CAT (H) : CAT CGT CAC CAC CAT (0.9482) - 116 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 117 3 CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA CAA CAA (1.0000) - 118 4 AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) AAC (N) : AAC AAC AAC AAC AAC (0.9999) - 119 1 AGA (R) AGA (R) AGA (R) AAA (K) AGA (R) AGA (R) AGA (R) : AGA AGA AGA AGA AGA (0.9748) - 120 4 GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) GAT (D) : GAT GAT GAT GAT GAT (0.9998) - 121 1 GTC (V) CTC (L) GTC (V) GTC (V) GTC (V) GTC (V) GTC (V) : GTC GTC GTC GTC GTC (0.9981) - 122 1 CGT (R) CGT (R) AGT (S) AGT (S) AGT (S) AGT (S) AGT (S) : AGT CGT AGT AGT AGT (0.9920) - 123 2 CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) CAG (Q) : CAG CAG CAG CAG CAG (1.0000) - 124 1 TAT (Y) TAT (Y) TAT (Y) TAC (Y) TAT (Y) TAT (Y) TAT (Y) : TAT TAT TAT TAT TAT (0.9932) - 125 1 GTT (V) ATT (I) GTT (V) GTT (V) GTT (V) GTT (V) GTT (V) : GTT GTT GTT GTT GTT (0.9882) - 126 1 CAA (Q) CAA (Q) GAA (E) AAA (K) CAA (Q) CAA (Q) CAA (Q) : CAA CAA CAA GAA CAA (0.5165) - 127 1 GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) GGT (G) : GGT GGT GGT GGT GGT (0.9998) - 128 7 TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) TGT (C) : TGT TGT TGT TGT TGT (1.0000) - 129 5 GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) GGA (G) : GGA GGA GGA GGA GGA (0.9999) - 130 1 GTG (V) GTA (V) GTA (V) GTG (V) GTG (V) GTA (V) GTA (V) : GTG GTG GTG GTG GTA (0.7827) - - -List of extant and reconstructed sequences - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -node #8 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #9 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -node #10 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -node #11 AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTG -node #12 AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - diff --git a/t/data/codeml_lysozyme/rst1 b/t/data/codeml_lysozyme/rst1 deleted file mode 100644 index 205f0ed9b..000000000 --- a/t/data/codeml_lysozyme/rst1 +++ /dev/null @@ -1 +0,0 @@ - 1 -0.00 0.511 0.489 -1.000 0.52 0.00 diff --git a/t/data/codeml_lysozyme/rub b/t/data/codeml_lysozyme/rub deleted file mode 100644 index c9fb6061e..000000000 --- a/t/data/codeml_lysozyme/rub +++ /dev/null @@ -1,48 +0,0 @@ - - -TREE # 1 - - 1 57.0511 911.866966 x: 0.06268 0.02434 0.03918 0.04580 0.06920 0.04580 0.05520 0.02250 0.11892 0.03972 0.02397 2.00271 0.99739 1.00045 - 2 18.9464 911.763959 x: 0.06764 0.02691 0.03838 0.04277 0.07495 0.04374 0.05085 0.02078 0.12004 0.03946 0.02493 2.00731 0.99290 1.00125 - 3 17.2055 911.691402 x: 0.06952 0.02343 0.03790 0.04130 0.07813 0.04241 0.05090 0.02232 0.12022 0.03952 0.02308 2.01485 0.98551 1.00259 - 4 41.0047 910.628609 x: 0.07137 0.02620 0.04439 0.03804 0.09645 0.03989 0.07654 0.01714 0.11898 0.04587 0.02567 2.18502 0.81862 1.03300 - 5 330.0384 908.660991 x: 0.07033 0.03282 0.03599 0.04791 0.09682 0.04206 0.07188 0.02569 0.11667 0.03794 0.02291 2.45879 0.55009 1.08221 - 6 273.9810 908.174440 x: 0.06841 0.02641 0.03736 0.04422 0.09012 0.04075 0.06501 0.01808 0.11687 0.04088 0.02517 2.53001 0.48216 1.09516 - 7 32.0852 908.121354 x: 0.06962 0.02714 0.04113 0.04201 0.08801 0.04202 0.06373 0.01990 0.11788 0.04271 0.02403 2.53971 0.47611 1.09709 - 8 10.2883 908.049989 x: 0.07394 0.02754 0.03882 0.04039 0.08345 0.04272 0.06595 0.01893 0.12390 0.04249 0.02214 2.56256 0.47895 1.10243 - 9 43.9147 907.929599 x: 0.07633 0.02582 0.03897 0.04193 0.08067 0.04109 0.06609 0.02170 0.13092 0.04309 0.02766 2.60763 0.48889 1.11319 - 10 113.4636 907.253062 x: 0.06522 0.02536 0.04672 0.04661 0.08046 0.03475 0.05796 0.01902 0.14707 0.03974 0.02253 2.85340 0.55093 1.17235 - 11 321.0222 906.555179 x: 0.05575 0.02365 0.04095 0.03870 0.08148 0.04813 0.04995 0.01976 0.14572 0.04344 0.02458 3.11682 0.61923 1.23610 - 12 218.4010 905.867140 x: 0.06763 0.02337 0.04059 0.04004 0.07126 0.04482 0.04620 0.01794 0.11796 0.04643 0.02419 3.36606 0.68506 1.29708 - 13 10.3815 905.858148 x: 0.06797 0.02299 0.04143 0.03927 0.07104 0.04529 0.04644 0.01777 0.11741 0.04411 0.02477 3.36949 0.68592 1.29825 - 14 0.9990 904.942858 x: 0.07115 0.02876 0.03573 0.04652 0.08159 0.04513 0.05585 0.02212 0.11829 0.03704 0.02354 3.94359 0.69088 2.38587 - 15 0.3806 904.698026 x: 0.07011 0.02501 0.04000 0.04494 0.07830 0.04277 0.05139 0.01930 0.12412 0.04343 0.02357 4.29118 0.68983 2.81855 - 16 0.2244 904.645420 x: 0.06969 0.02541 0.03882 0.04333 0.07840 0.04396 0.05141 0.01939 0.12040 0.04029 0.02387 4.54266 0.68846 3.09347 - 17 0.0853 904.640565 x: 0.06999 0.02558 0.03888 0.04375 0.07907 0.04392 0.05259 0.01951 0.12142 0.04125 0.02378 4.58691 0.68596 3.19513 - 18 0.0476 904.639140 x: 0.07001 0.02561 0.03907 0.04408 0.07910 0.04381 0.05186 0.01956 0.12174 0.04098 0.02376 4.60048 0.68393 3.28862 - 19 0.0549 904.636957 x: 0.07016 0.02550 0.03890 0.04390 0.07906 0.04381 0.05212 0.01934 0.12067 0.04109 0.02378 4.57807 0.68577 3.47164 - 20 0.0294 904.636560 x: 0.07006 0.02557 0.03891 0.04387 0.07901 0.04390 0.05216 0.01948 0.12134 0.04102 0.02378 4.56178 0.68562 3.50174 - 21 0.0035 904.636554 x: 0.07001 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12130 0.04104 0.02378 4.56086 0.68574 3.50529 - 22 0.0004 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56116 0.68580 3.50580 - 23 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56117 0.68580 3.50577 - 24 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 - 25 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575 - -TREE # 2 - - 1 64.8459 904.711965 x: 0.06603 0.02485 0.04005 0.04745 0.07283 0.04652 0.05480 0.01985 0.11993 0.04141 0.02359 4.56116 0.68595 3.50574 - 2 17.6419 904.639797 x: 0.07001 0.02633 0.03883 0.04446 0.07825 0.04417 0.05145 0.01925 0.12104 0.04098 0.02420 4.56116 0.68598 3.50574 - 3 4.6734 904.636959 x: 0.07020 0.02548 0.03884 0.04411 0.07884 0.04400 0.05172 0.01950 0.12114 0.04097 0.02372 4.56116 0.68598 3.50574 - 4 1.3499 904.636631 x: 0.07016 0.02554 0.03899 0.04395 0.07907 0.04400 0.05210 0.01938 0.12122 0.04106 0.02378 4.56116 0.68597 3.50574 - 5 0.3002 904.636616 x: 0.07014 0.02557 0.03898 0.04399 0.07911 0.04400 0.05213 0.01944 0.12126 0.04106 0.02378 4.56116 0.68597 3.50574 - 6 0.1248 904.636613 x: 0.07012 0.02556 0.03896 0.04401 0.07913 0.04399 0.05213 0.01942 0.12130 0.04105 0.02378 4.56116 0.68597 3.50574 - 7 0.0510 904.636612 x: 0.07011 0.02556 0.03898 0.04400 0.07912 0.04399 0.05212 0.01943 0.12132 0.04106 0.02378 4.56116 0.68597 3.50574 - 8 0.0209 904.636612 x: 0.07011 0.02556 0.03897 0.04400 0.07912 0.04399 0.05212 0.01943 0.12133 0.04106 0.02378 4.56116 0.68596 3.50574 - 9 0.0161 904.636612 x: 0.07012 0.02556 0.03897 0.04400 0.07911 0.04399 0.05212 0.01943 0.12134 0.04106 0.02378 4.56116 0.68596 3.50574 - 10 0.0156 904.636611 x: 0.07012 0.02556 0.03898 0.04401 0.07911 0.04398 0.05212 0.01943 0.12134 0.04105 0.02378 4.56116 0.68592 3.50574 - 11 0.0916 904.636598 x: 0.07010 0.02556 0.03896 0.04398 0.07911 0.04397 0.05212 0.01943 0.12132 0.04105 0.02378 4.56121 0.68506 3.50574 - 12 0.0063 904.636596 x: 0.07009 0.02557 0.03896 0.04398 0.07911 0.04396 0.05212 0.01944 0.12132 0.04108 0.02377 4.56122 0.68508 3.50574 - 13 0.0706 904.636554 x: 0.07001 0.02557 0.03893 0.04387 0.07905 0.04388 0.05214 0.01948 0.12131 0.04103 0.02378 4.56129 0.68581 3.50574 - 14 0.0001 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56124 0.68581 3.50574 - 15 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 - 16 0.0000 904.636553 x: 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574 \ No newline at end of file diff --git a/t/data/codeml_nan.mlc b/t/data/codeml_nan.mlc deleted file mode 100644 index 63ded125c..000000000 --- a/t/data/codeml_nan.mlc +++ /dev/null @@ -1,177 +0,0 @@ - -seed used = 785596301 - - -Data set 1 - 3 141 - -all_s57600 CTC TTC CAC ACC TCC CAC TCC CCC CCC CTC CAC TCC TTC TTC ACC TCC CCT TCC CCC TCC CTC CTT CCC TCC CCC ACC CTC TTC CTT TTC CCC TTC CAC TCC CCC TTC CTC CGC CTC CCC TCC CTC CCC CCC CAC CAC CCC -all_s56012 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CTC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC -all_c11513 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CCC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC - - - -Printing out site pattern counts - - - 11 93 P - -all_s57600 ACC CAC CAC CAC CAC CCC CCC CCC CCC CCC CCC CCT CGC CTC CTC CTC CTC CTC CTC CTT CTT TCC TCC TCC TCC TCC TCC TCC TTC TTC TTC -all_s56012 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... ... ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ... -all_c11513 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... .C. ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ... - - 3 3 1 1 1 1 5 1 1 1 2 1 1 1 1 - 2 1 1 1 1 1 1 1 1 1 3 1 1 1 5 - 1 - -CODONML (in paml version 4.4, January 2010) /scratch/davepaml17/cluster45_fake.phy -Model: One dN/dS ratio for branches Global clock -Codon frequency model: F3x4 -ns = 3 ls = 47 - -Codon usage in sequences --------------------------------------------------------------------------------------------------------------- -Phe TTT 0 0 0 1 0 0 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 0 | Cys TGT 0 0 0 0 0 0 - TTC 7 7 7 7 9 7 | TCC 9 10 8 10 8 9 | TAC 0 0 0 0 0 0 | TGC 0 0 0 0 0 0 -Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 - TTG 0 0 0 0 0 0 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Leu CTT 2 1 1 2 1 0 | Pro CCT 1 0 0 0 0 0 | His CAT 0 0 0 0 0 0 | Arg CGT 0 0 0 0 1 0 - CTC 7 9 4 6 8 10 | CCC 11 11 19 12 13 12 | CAC 6 5 4 5 4 5 | CGC 1 1 1 0 0 1 - CTA 0 0 0 0 0 0 | CCA 0 0 0 0 0 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 - CTG 0 0 0 0 0 0 | CCG 0 0 0 0 0 0 | CAG 0 0 0 0 0 0 | CGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Ile ATT 0 0 0 0 0 0 | Thr ACT 0 0 0 0 0 0 | Asn AAT 0 0 0 0 0 0 | Ser AGT 0 0 0 0 0 0 - ATC 0 0 0 0 0 0 | ACC 3 3 3 4 3 3 | AAC 0 0 0 0 0 0 | AGC 0 0 0 0 0 0 - ATA 0 0 0 0 0 0 | ACA 0 0 0 0 0 0 | Lys AAA 0 0 0 0 0 0 | Arg AGA 0 0 0 0 0 0 -Met ATG 0 0 0 0 0 0 | ACG 0 0 0 0 0 0 | AAG 0 0 0 0 0 0 | AGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Val GTT 0 0 0 0 0 0 | Ala GCT 0 0 0 0 0 0 | Asp GAT 0 0 0 0 0 0 | Gly GGT 0 0 0 0 0 0 - GTC 0 0 0 0 0 0 | GCC 0 0 0 0 0 0 | GAC 0 0 0 0 0 0 | GGC 0 0 0 0 0 0 - GTA 0 0 0 0 0 0 | GCA 0 0 0 0 0 0 | Glu GAA 0 0 0 0 0 0 | GGA 0 0 0 0 0 0 - GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- - --------------------------------------------------------------------------------------------------- -Phe TTT 0 0 0 0 0 | Ser TCT 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 | Cys TGT 0 0 0 0 0 - TTC 7 8 9 7 7 | TCC 9 12 9 10 10 | TAC 0 0 0 0 0 | TGC 0 0 0 0 0 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 0 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 0 0 0 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Leu CTT 0 1 1 1 1 | Pro CCT 0 0 1 0 0 | His CAT 0 0 1 0 0 | Arg CGT 0 0 0 0 0 - CTC 9 8 6 9 9 | CCC 13 8 11 11 11 | CAC 5 5 5 5 5 | CGC 1 1 0 1 1 - CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 0 0 0 0 0 | CGA 0 0 0 0 0 - CTG 0 0 0 0 0 | CCG 0 0 0 0 0 | CAG 0 0 0 0 0 | CGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 0 0 0 | Thr ACT 0 0 0 0 0 | Asn AAT 0 0 0 0 0 | Ser AGT 0 0 0 0 0 - ATC 0 0 0 0 0 | ACC 3 4 4 3 3 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0 - ATA 0 0 0 0 0 | ACA 0 0 0 0 0 | Lys AAA 0 0 0 0 0 | Arg AGA 0 0 0 0 0 -Met ATG 0 0 0 0 0 | ACG 0 0 0 0 0 | AAG 0 0 0 0 0 | AGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- -Val GTT 0 0 0 0 0 | Ala GCT 0 0 0 0 0 | Asp GAT 0 0 0 0 0 | Gly GGT 0 0 0 0 0 - GTC 0 0 0 0 0 | GCC 0 0 0 0 0 | GAC 0 0 0 0 0 | GGC 0 0 0 0 0 - GTA 0 0 0 0 0 | GCA 0 0 0 0 0 | Glu GAA 0 0 0 0 0 | GGA 0 0 0 0 0 - GTG 0 0 0 0 0 | GCG 0 0 0 0 0 | GAG 0 0 0 0 0 | GGG 0 0 0 0 0 --------------------------------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: all_s57600 -position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 -position 2: T:0.34043 C:0.51064 A:0.12766 G:0.02128 -position 3: T:0.06383 C:0.93617 A:0.00000 G:0.00000 -Average T:0.24823 C:0.68085 A:0.06383 G:0.00709 - -#2: all_s56012 -position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 -position 2: T:0.36170 C:0.51064 A:0.10638 G:0.02128 -position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000 -Average T:0.23404 C:0.70213 A:0.05674 G:0.00709 - -#3: all_c11513 -position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000 -position 2: T:0.34043 C:0.53191 A:0.10638 G:0.02128 -position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000 -Average T:0.22695 C:0.70922 A:0.05674 G:0.00709 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 1 | Ser S TCT 0 | Tyr Y TAT 0 | Cys C TGT 0 - TTC 82 | TCC 104 | TAC 0 | TGC 0 -Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 11 | Pro P CCT 2 | His H CAT 1 | Arg R CGT 1 - CTC 85 | CCC 132 | CAC 54 | CGC 8 - CTA 0 | CCA 0 | Gln Q CAA 0 | CGA 0 - CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 - ATC 0 | ACC 36 | AAC 0 | AGC 0 - ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 -Met M ATG 0 | ACG 0 | AAG 0 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 - GTC 0 | GCC 0 | GAC 0 | GGC 0 - GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 - GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.36170 C:0.56867 A:0.06963 G:0.00000 -position 2: T:0.34623 C:0.52998 A:0.10638 G:0.01741 -position 3: T:0.03095 C:0.96905 A:0.00000 G:0.00000 -Average T:0.24629 C:0.68923 A:0.05867 G:0.00580 - -Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): - 0.00387564 0.12135585 0.00000000 0.00000000 - 0.00593254 0.18576259 0.00000000 0.00000000 - 0.00119084 0.03728811 0.00000000 0.00000000 - 0.00019486 0.00610169 0.00000000 0.00000000 - 0.00609325 0.19079477 0.00000000 0.00000000 - 0.00932709 0.29205456 0.00000000 0.00000000 - 0.00187223 0.05862409 0.00000000 0.00000000 - 0.00030636 0.00959303 0.00000000 0.00000000 - 0.00074611 0.02336262 0.00000000 0.00000000 - 0.00114209 0.03576178 0.00000000 0.00000000 - 0.00022925 0.00717846 0.00000000 0.00000000 - 0.00003751 0.00117466 0.00000000 0.00000000 - 0.00000000 0.00000000 0.00000000 0.00000000 - 0.00000000 0.00000000 0.00000000 0.00000000 - 0.00000000 0.00000000 0.00000000 0.00000000 - 0.00000000 0.00000000 0.00000000 0.00000000 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later ML. analysis. -Use runmode = -2 for ML pairwise comparison.) - -all_s57600 -all_s56012 0.8758 (0.0717 0.0819) -all_c11513 1.0080 (0.0826 0.0819) 0.7616 (0.0199 0.0261) - -pairwise comparison, codon frequencies: F3x4. - - -2 (all_c56012) ... 1 (all_s57600) -lnL = -126.880601 - 0.19045 2.92330 0.10941 - -t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353 - - -3 (all_c11513) ... 1 (all_c57600) -lnL = -142.636697 - 4.21113 0.72684 0.00175 - -t= 4.2111 S= 4.2 N= 136.8 dN/dS= 0.0018 dN= 0.0789 dS=44.9635 - - -3 (all_c11513) ... 2 (all_s56012) -lnL = -93.410530 - 0.02176 999.00000 0.13702 - -t= 0.0218 S= 0.0 N= 141.0 dN/dS= 0.1370 dN= 0.0073 dS= nan diff --git a/t/data/codeml_nssites.mlc b/t/data/codeml_nssites.mlc deleted file mode 100644 index bd15f69dd..000000000 --- a/t/data/codeml_nssites.mlc +++ /dev/null @@ -1,329 +0,0 @@ - -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG -Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA -Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA -Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG -Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG -Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA -Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA - - -CODONML (in paml 3.13, August 2002) lysozymeSmall.txt Model: One dN/dS ratio dGamma (ncatG=11) -Codon frequencies: F3x4 -Warning: Gamma model for codons. See documentation.Site-class models - -ns = 7 ls = 130 -# site patterns = 81 - 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1 - 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1 - 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1 - 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 - -1 -Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG -Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A -Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A -Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ... -Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ... -Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A -Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A - -Codon usage in sequences --------------------------------------------------------------------------------------------------------------- -Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7 - TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1 -Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 - TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5 --------------------------------------------------------------------------------------------------------------- -Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2 - CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0 - CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0 - CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2 - ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3 - ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4 -Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4 --------------------------------------------------------------------------------------------------------------- -Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1 - GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3 - GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5 - GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1 --------------------------------------------------------------------------------------------------------------- - --------------------------------------------------- -Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7 - TTC 0 | TCC 1 | TAC 2 | TGC 1 -Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0 - TTG 3 | TCG 0 | TAG 0 | Trp TGG 5 --------------------------------------------------- -Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1 - CTC 0 | CCC 0 | CAC 1 | CGC 1 - CTA 1 | CCA 2 | Gln CAA 5 | CGA 0 - CTG 3 | CCG 0 | CAG 2 | CGG 0 --------------------------------------------------- -Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2 - ATC 3 | ACC 1 | AAC 5 | AGC 3 - ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3 -Met ATG 1 | ACG 0 | AAG 2 | AGG 5 --------------------------------------------------- -Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1 - GTC 3 | GCC 4 | GAC 2 | GGC 3 - GTA 1 | GCA 5 | Glu GAA 2 | GGA 5 - GTG 2 | GCG 0 | GAG 2 | GGG 1 --------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: Hsa_Human -position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615 -position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#2: Hla_gibbon -position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308 -position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308 -position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462 - -#3: Cgu/Can_colobus -position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385 -position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#4: Pne_langur -position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154 -position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 -position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231 - -#5: Mmu_rhesus -position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538 -position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 -position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 - -#6: Ssc_squirrelM -position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077 -position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 -position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231 - -#7: Cja_marmoset -position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846 -position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 -position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49 - TTC 1 | TCC 7 | TAC 21 | TGC 7 -Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35 ------------------------------------------------------------------------------- -Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8 - CTC 1 | CCC 0 | CAC 6 | CGC 6 - CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4 - CTG 18 | CCG 0 | CAG 14 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17 - ATC 22 | ACC 7 | AAC 35 | AGC 21 - ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28 -Met M ATG 7 | ACG 0 | AAG 17 | AGG 22 ------------------------------------------------------------------------------- -Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11 - GTC 19 | GCC 24 | GAC 10 | GGC 21 - GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35 - GTG 15 | GCG 0 | GAG 14 | GGG 7 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846 -position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780 -position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231 - -Codon frequencies under model, for use in evolver: - 0.01378574 0.00962226 0.01059374 0.00809565 - 0.01181635 0.00824765 0.00908035 0.00693913 - 0.02279949 0.01591374 0.00000000 0.00000000 - 0.02052711 0.01432765 0.00000000 0.01205451 - 0.00941649 0.00657258 0.00723616 0.00552982 - 0.00807127 0.00563364 0.00620242 0.00473984 - 0.01557342 0.01087004 0.01196749 0.00914546 - 0.01402125 0.00978665 0.01077472 0.00823396 - 0.02214758 0.01545871 0.01701945 0.01300613 - 0.01898364 0.01325032 0.01458810 0.01114811 - 0.03662868 0.02556633 0.02814755 0.02151013 - 0.03297798 0.02301819 0.02534214 0.01936627 - 0.02320222 0.01619484 0.01782990 0.01362547 - 0.01988762 0.01388129 0.01528277 0.01167897 - 0.03837291 0.02678377 0.02948791 0.02253443 - 0.03454836 0.02411429 0.02654891 0.02028847 - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -Hsa_Human -Hla_gibbon 0.2782 (0.0133 0.0478) -Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671) -Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484) -Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364) -Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230) -Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619) - - -Model 0: one-ratio - -TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 -check convergence.. -lnL(ntime: 11 np: 14): -906.017440 +0.000000 - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - 0.06798 0.02556 0.03889 0.04345 0.07637 0.04379 0.05254 0.02168 0.12266 0.04080 0.02392 4.54006 0.80663 0.50000 -SEs for parameters: - 0.02557 0.01516 0.01844 0.02016 0.02668 0.01990 0.02155 0.01551 0.03392 0.01916 0.01506 0.23600 0.23600 -1.00000 -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.55765 - -((1: 0.02556, 2: 0.03889): 0.06798, ((3: 0.04379, 4: 0.05254): 0.07637, 5: 0.02168): 0.04345, (6: 0.04080, 7: 0.02392): 0.12266); - -((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254): 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266); - -Detailed output identifying parameters -kappa (ts/tv) = 4.54006 - -alpha (gamma) = 0.50000 -r ( 1): 1.00000 -f: 1.00000 - -dN & dS for each branch - - branch t S N dN/dS dN dS S*dS N*dN - - 8..9 0.068 107.8 282.2 0.8066 0.0213 0.0263 2.8 6.0 - 9..1 0.026 107.8 282.2 0.8066 0.0080 0.0099 1.1 2.3 - 9..2 0.039 107.8 282.2 0.8066 0.0122 0.0151 1.6 3.4 - 8..10 0.043 107.8 282.2 0.8066 0.0136 0.0168 1.8 3.8 - 10..11 0.076 107.8 282.2 0.8066 0.0239 0.0296 3.2 6.7 - 11..3 0.044 107.8 282.2 0.8066 0.0137 0.0170 1.8 3.9 - 11..4 0.053 107.8 282.2 0.8066 0.0164 0.0204 2.2 4.6 - 10..5 0.022 107.8 282.2 0.8066 0.0068 0.0084 0.9 1.9 - 8..12 0.123 107.8 282.2 0.8066 0.0383 0.0475 5.1 10.8 - 12..6 0.041 107.8 282.2 0.8066 0.0128 0.0158 1.7 3.6 - 12..7 0.024 107.8 282.2 0.8066 0.0075 0.0093 1.0 2.1 - - -Time used: 00:02:05 - - -Model 1: neutral (2 categories) - -TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 -lnL(ntime: 11 np: 14): -902.503869 +0.000000 - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - 0.06961 0.02556 0.03938 0.04422 0.07778 0.04414 0.05228 0.02134 0.12574 0.04157 0.02367 4.29790 0.41271 0.50000 -SEs for parameters: - 0.02665 0.01541 0.01888 0.02101 0.02769 0.02034 0.02188 0.01585 0.03565 0.01971 0.01530 -1.00000 -1.00000 -1.00000 -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.56528 - -((1: 0.02556, 2: 0.03938): 0.06961, ((3: 0.04414, 4: 0.05228): 0.07778, 5: 0.02134): 0.04422, (6: 0.04157, 7: 0.02367): 0.12574); - -((Hsa_Human: 0.02556, Hla_gibbon: 0.03938): 0.06961, ((Cgu/Can_colobus: 0.04414, Pne_langur: 0.05228): 0.07778, Mmu_rhesus: 0.02134): 0.04422, (Ssc_squirrelM: 0.04157, Cja_marmoset: 0.02367): 0.12574); - -Detailed output identifying parameters -kappa (ts/tv) = 4.29790 - - -dN/dS for site classes (K=2) -p: 0.41271 0.58729 -w: 0.00000 1.00000 - -alpha (gamma) = 0.41271 -r ( 2): 0.00000 1.00000 -f: 0.41271 0.58729 - -dN & dS for each branch - - branch t S N dN/dS dN dS S*dS N*dN - - 8..9 0.070 107.1 282.9 0.5873 0.0195 0.0331 3.5 5.5 - 9..1 0.026 107.1 282.9 0.5873 0.0071 0.0122 1.3 2.0 - 9..2 0.039 107.1 282.9 0.5873 0.0110 0.0187 2.0 3.1 - 8..10 0.044 107.1 282.9 0.5873 0.0124 0.0210 2.3 3.5 - 10..11 0.078 107.1 282.9 0.5873 0.0217 0.0370 4.0 6.1 - 11..3 0.044 107.1 282.9 0.5873 0.0123 0.0210 2.2 3.5 - 11..4 0.052 107.1 282.9 0.5873 0.0146 0.0249 2.7 4.1 - 10..5 0.021 107.1 282.9 0.5873 0.0060 0.0102 1.1 1.7 - 8..12 0.126 107.1 282.9 0.5873 0.0351 0.0598 6.4 9.9 - 12..6 0.042 107.1 282.9 0.5873 0.0116 0.0198 2.1 3.3 - 12..7 0.024 107.1 282.9 0.5873 0.0066 0.0113 1.2 1.9 - - -Time used: 00:05:26 - - -Model 2: selection (3 categories) - -TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 -check convergence.. -lnL(ntime: 11 np: 16): -900.076500 +0.000000 - 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 - 0.07903 0.02598 0.04137 0.04535 0.08550 0.04486 0.05417 0.01935 0.13948 0.04319 0.02492 5.12250 0.38160 0.54916 6.17292 0.41271 -SEs for parameters: - 0.03226 0.01618 0.02021 0.02390 0.03229 0.02158 0.02363 0.01746 0.04358 0.02088 0.01602 1.50414 0.14016 0.16630 4.30113 -1.00000 -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.60321 - -((1: 0.02598, 2: 0.04137): 0.07903, ((3: 0.04486, 4: 0.05417): 0.08550, 5: 0.01935): 0.04535, (6: 0.04319, 7: 0.02492): 0.13948); - -((Hsa_Human: 0.02598, Hla_gibbon: 0.04137): 0.07903, ((Cgu/Can_colobus: 0.04486, Pne_langur: 0.05417): 0.08550, Mmu_rhesus: 0.01935): 0.04535, (Ssc_squirrelM: 0.04319, Cja_marmoset: 0.02492): 0.13948); - -Detailed output identifying parameters -kappa (ts/tv) = 5.12250 - - -dN/dS for site classes (K=3) -p: 0.38160 0.54916 0.06924 -w: 0.00000 1.00000 6.17292 - -alpha (gamma) = 0.38160 -r ( 3): 0.00000 1.00000 6.17292 -f: 0.38160 0.54916 0.06924 - -dN & dS for each branch - - branch t S N dN/dS dN dS S*dS N*dN - - 8..9 0.079 109.3 280.7 0.9766 0.0262 0.0268 2.9 7.3 - 9..1 0.026 109.3 280.7 0.9766 0.0086 0.0088 1.0 2.4 - 9..2 0.041 109.3 280.7 0.9766 0.0137 0.0140 1.5 3.8 - 8..10 0.045 109.3 280.7 0.9766 0.0150 0.0154 1.7 4.2 - 10..11 0.086 109.3 280.7 0.9766 0.0283 0.0290 3.2 7.9 - 11..3 0.045 109.3 280.7 0.9766 0.0149 0.0152 1.7 4.2 - 11..4 0.054 109.3 280.7 0.9766 0.0179 0.0184 2.0 5.0 - 10..5 0.019 109.3 280.7 0.9766 0.0064 0.0066 0.7 1.8 - 8..12 0.139 109.3 280.7 0.9766 0.0462 0.0473 5.2 13.0 - 12..6 0.043 109.3 280.7 0.9766 0.0143 0.0146 1.6 4.0 - 12..7 0.025 109.3 280.7 0.9766 0.0083 0.0085 0.9 2.3 - - - -Positively selected sites Prob(w>1): - - 15 L 0.6588 - 17 M 0.6601 - 37 G 0.7155 - 41 R 0.9282 - 50 R 0.8292 - 62 R 0.5229 - 114 N 0.6491 - 126 Q 0.5226 - - -Time used: 00:13:43 diff --git a/t/data/singleNSsite.mlc b/t/data/singleNSsite.mlc deleted file mode 100644 index d39f62226..000000000 --- a/t/data/singleNSsite.mlc +++ /dev/null @@ -1,152 +0,0 @@ -CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio -Codon frequencies: F3x4 -Site-class models: PositiveSelection -ns = 3 ls = 6 - -Codon usage in sequences --------------------------------------------------------------------------- -Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0 - TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0 -Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0 - TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0 --------------------------------------------------------------------------- -Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0 - CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0 - CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0 - CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0 --------------------------------------------------------------------------- -Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0 - ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0 - ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0 -Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0 --------------------------------------------------------------------------- -Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0 - GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0 - GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0 - GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0 --------------------------------------------------------------------------- - -Codon position x base (3x4) table for each sequence. - -#1: test0 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#2: test1 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333 - -#3: test2 -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000 -position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333 - -Sums of codon usage counts ------------------------------------------------------------------------------- -Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0 - TTC 0 | TCC 1 | TAC 0 | TGC 0 -Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0 - TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0 ------------------------------------------------------------------------------- -Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0 - CTC 0 | CCC 1 | CAC 0 | CGC 0 - CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0 - CTG 0 | CCG 0 | CAG 0 | CGG 0 ------------------------------------------------------------------------------- -Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0 - ATC 0 | ACC 0 | AAC 0 | AGC 0 - ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0 -Met M ATG 4 | ACG 2 | AAG 0 | AGG 0 ------------------------------------------------------------------------------- -Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0 - GTC 0 | GCC 0 | GAC 0 | GGC 0 - GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0 - GTG 0 | GCG 0 | GAG 0 | GGG 0 ------------------------------------------------------------------------------- - - -Codon position x base (3x4) table, overall - -position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000 -position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000 -position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333 - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later m.l. analysis. -Use runmode = -2 for ML pairwise comparison.) - -test0 -test1 -1.0000 (0.0706 0.0000) -test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745) - - -TREE # 1: (1, 2, 3); MP score: 3 -check convergence.. -lnL(ntime: 3 np: 8): -30.819156 +0.000000 - 4..1 4..2 4..3 - 0.25573 0.00000 0.62424 5.28487 1.00000 0.00000 0.09213 1.00000 - -Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). - -tree length = 0.87997 - -(1: 0.255727, 2: 0.000004, 3: 0.624239); - -(test0: 0.255727, test1: 0.000004, test2: 0.624239); - -Detailed output identifying parameters - -kappa (ts/tv) = 5.28487 - - -dN/dS for site classes (K=3) - -p: 1.00000 0.00000 0.00000 -w: 0.09213 1.00000 1.00000 - -dN & dS for each branch - - branch t N S dN/dS dN dS N*dN S*dS - - 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2 - 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0 - 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0 - - -Naive Empirical Bayes (NEB) analysis -Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) -Positively selected sites (*: P>95%; **: P>99%) - - Pr(w>1) post mean +- SE for w - - - - -The grid (see ternary graph for p0-p1) - -w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 -w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 - - -Posterior on the grid - -w0: 0.402 0.260 0.147 0.081 0.045 0.026 0.016 0.010 0.007 0.005 -w2: 0.138 0.114 0.104 0.098 0.095 0.093 0.091 0.090 0.089 0.088 - -Posterior for p0-p1 (see the ternary graph) - - 0.001 - 0.001 0.002 0.003 - 0.001 0.001 0.002 0.003 0.006 - 0.000 0.001 0.001 0.002 0.004 0.006 0.010 - 0.000 0.000 0.001 0.001 0.003 0.004 0.007 0.011 0.016 - 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.008 0.012 0.017 0.025 - 0.000 0.000 0.000 0.001 0.001 0.002 0.004 0.006 0.009 0.013 0.019 0.026 0.036 - 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.004 0.006 0.009 0.014 0.019 0.027 0.037 0.049 - 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.014 0.020 0.028 0.037 0.049 0.063 - 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.015 0.020 0.027 0.036 0.046 0.061 0.075 - -sum of density on p0-p1 = 1.000000 diff --git a/t/data/yn00.mlc b/t/data/yn00.mlc deleted file mode 100644 index 03618af1e..000000000 --- a/t/data/yn00.mlc +++ /dev/null @@ -1,106 +0,0 @@ -YN00 examples/abglobin.nuc - -ns = 5 ls = 285 - -Codon position x base (3x4) table for each sequence. - -human -position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649 -position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333 -position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140 - -goat-cow -position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000 -position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035 -position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088 - -rabbit -position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140 -position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684 -position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439 - -rat -position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895 -position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439 -position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421 - -marsupial -position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439 -position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333 -position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123 - -Average -position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825 -position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965 -position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842 - -Codon usage for each species --------------------------------------------------------------------------------------------------- -Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2 - TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3 -Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 - TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4 --------------------------------------------------------------------------------------------------- -Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1 - CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0 - CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0 - CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0 --------------------------------------------------------------------------------------------------- -Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1 - ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3 - ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2 -Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2 --------------------------------------------------------------------------------------------------- -Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10 - GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5 - GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3 - GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2 --------------------------------------------------------------------------------------------------- - - -Sums --------------------------------------------------- -Phe TTT 25 | Ser TCT 25 | Tyr TAT 10 | Cys TGT 8 - TTC 51 | TCC 31 | TAC 19 | TGC 9 -Leu TTA 0 | TCA 1 | *** TAA 0 | *** TGA 0 - TTG 12 | TCG 3 | TAG 0 | Trp TGG 16 --------------------------------------------------- -Leu CTT 6 | Pro CCT 23 | His CAT 21 | Arg CGT 7 - CTC 24 | CCC 25 | CAC 68 | CGC 1 - CTA 6 | CCA 3 | Gln CAA 1 | CGA 0 - CTG 123 | CCG 5 | CAG 25 | CGG 2 --------------------------------------------------- -Ile ATT 6 | Thr ACT 24 | Asn AAT 16 | Ser AGT 13 - ATC 12 | ACC 53 | AAC 35 | AGC 19 - ATA 1 | ACA 2 | Lys AAA 20 | Arg AGA 3 -Met ATG 17 | ACG 0 | AAG 98 | AGG 17 --------------------------------------------------- -Val GTT 24 | Ala GCT 50 | Asp GAT 31 | Gly GGT 30 - GTC 19 | GCC 92 | GAC 48 | GGC 60 - GTA 2 | GCA 7 | Glu GAA 19 | GGA 7 - GTG 89 | GCG 14 | GAG 40 | GGG 7 --------------------------------------------------- - - -Nei & Gojobori 1986. dN/dS (dN, dS) -human -goat-cow 0.251(0.0863 0.3443) -rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581) -rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187) -marsupial 0.190(0.1931 1.0148) 0.189(0.1910 1.0099) 0.218(0.2111 0.9668) 0.272(0.2404 0.8852) - -Estimation by the method of Yang & Nielsen (2000): -(equal weighting of pathways) - -seq. seq. S N t kappa omega dN +- SE dS +- SE - - 2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 +- 0.0115 0.5031 +- 0.0930 - 3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 +- 0.0114 0.4967 +- 0.0927 - 3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 +- 0.0128 0.5169 +- 0.0925 - 4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 +- 0.0144 0.9301 +- 0.1987 - 4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 +- 0.0159 0.9297 +- 0.2091 - 4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 +- 0.0149 1.0286 +- 0.2614 - 5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 +- 0.0184 2.6055 +- 3.9344 - 5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 +- 0.0184 1.3008 +- 0.1995 - 5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 +- 0.0194 1.3020 +- 0.2026 - 5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 +- 0.0215 1.4797 +- 0.5173 diff --git a/t/data/yn00_45.mlc b/t/data/yn00_45.mlc deleted file mode 100644 index cf9182e1b..000000000 --- a/t/data/yn00_45.mlc +++ /dev/null @@ -1,595 +0,0 @@ -YN00 examples/small_taxon_set.nuc - -ns = 9 ls = 475 - -Codon position x base (3x4) table for each sequence. - -Pdel181_DNA2 -position 1: T:0.18105 C:0.19368 A:0.23579 G:0.38947 -position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 -position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 - -Pfre186_DNA2 -position 1: T:0.18105 C:0.19368 A:0.23789 G:0.38737 -position 2: T:0.26526 C:0.23158 A:0.30105 G:0.20211 -position 3: T:0.41895 C:0.15579 A:0.28211 G:0.14316 - -Pgra187_DNA2 -position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 -position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 -position 3: T:0.42105 C:0.15158 A:0.28632 G:0.14105 - -Phet26_DNA21 -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 - -Pmex37_DNA21 -position 1: T:0.18105 C:0.19158 A:0.23789 G:0.38947 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28211 G:0.14105 - -Ptre197_DNA2 -position 1: T:0.18105 C:0.19158 A:0.24000 G:0.38737 -position 2: T:0.26316 C:0.23158 A:0.30105 G:0.20421 -position 3: T:0.42316 C:0.15158 A:0.28421 G:0.14105 - -WHR1_DNA225 -position 1: T:0.18105 C:0.19158 A:0.23579 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41684 C:0.15579 A:0.28211 G:0.14526 - -YALD273_DNA5 -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 - -Pop_trich_ch -position 1: T:0.18105 C:0.19368 A:0.23368 G:0.39158 -position 2: T:0.26526 C:0.22947 A:0.30105 G:0.20421 -position 3: T:0.41895 C:0.15789 A:0.28632 G:0.13684 - -Average -position 1: T:0.18105 C:0.19275 A:0.23649 G:0.38971 -position 2: T:0.26480 C:0.23041 A:0.30105 G:0.20374 -position 3: T:0.41942 C:0.15579 A:0.28421 G:0.14058 - -Codon usage for each species --------------------------------------------------------------------------------------------------------------- -Phe TTT 14 14 14 14 14 14 | Ser TCT 6 6 6 6 6 6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT 5 5 5 5 5 5 - TTC 8 8 8 8 8 8 | TCC 4 4 4 4 4 4 | TAC 4 4 4 4 4 4 | TGC 3 3 3 3 3 3 -Leu TTA 9 9 9 9 9 9 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 - TTG 10 10 10 10 10 10 | TCG 1 1 1 1 1 1 | TAG 0 0 0 0 0 0 | Trp TGG 8 8 8 8 8 8 --------------------------------------------------------------------------------------------------------------- -Leu CTT 9 9 9 9 9 9 | Pro CCT 11 11 12 11 10 12 | His CAT 9 9 9 9 9 9 | Arg CGT 11 11 11 11 11 11 - CTC 0 0 0 0 0 0 | CCC 6 6 5 6 6 5 | CAC 5 5 5 5 5 5 | CGC 5 5 5 5 5 5 - CTA 9 9 9 10 9 9 | CCA 3 3 3 3 3 3 | Gln CAA 10 10 9 10 10 9 | CGA 6 6 6 6 6 6 - CTG 4 4 4 3 4 4 | CCG 2 2 2 2 2 2 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 --------------------------------------------------------------------------------------------------------------- -Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT 9 9 9 9 9 9 | Ser AGT 1 1 2 2 2 2 - ATC 9 9 7 9 9 8 | ACC 8 8 8 8 8 8 | AAC 6 6 6 6 6 6 | AGC 3 3 3 3 3 3 - ATA 1 1 4 2 1 3 | ACA 6 6 5 5 5 5 | Lys AAA 18 18 18 18 18 18 | Arg AGA 6 6 6 6 6 6 -Met ATG 10 10 10 9 10 10 | ACG 1 1 1 1 1 1 | AAG 6 6 6 6 6 6 | AGG 1 1 1 1 1 1 --------------------------------------------------------------------------------------------------------------- -Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23 - GTC 1 1 1 1 1 1 | GCC 5 5 5 5 5 4 | GAC 5 5 6 6 6 6 | GGC 2 2 2 2 2 2 - GTA 13 13 12 13 13 12 | GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 | GGA 13 13 13 13 13 13 - GTG 4 4 4 4 4 4 | GCG 0 0 0 0 0 0 | GAG 10 10 9 9 9 9 | GGG 9 9 9 9 9 9 --------------------------------------------------------------------------------------------------------------- - --------------------------------------------------------------------------- -Phe TTT 14 14 14 | Ser TCT 5 6 6 | Tyr TAT 13 13 13 | Cys TGT 5 5 5 - TTC 8 8 8 | TCC 5 4 4 | TAC 4 4 4 | TGC 3 3 3 -Leu TTA 9 9 9 | TCA 1 1 1 | *** TAA 0 0 0 | *** TGA 0 0 0 - TTG 10 10 10 | TCG 1 1 1 | TAG 0 0 0 | Trp TGG 8 8 8 --------------------------------------------------------------------------- -Leu CTT 9 9 9 | Pro CCT 10 11 11 | His CAT 9 9 9 | Arg CGT 11 11 11 - CTC 0 0 0 | CCC 6 6 6 | CAC 5 5 5 | CGC 5 5 5 - CTA 9 10 10 | CCA 3 3 3 | Gln CAA 10 10 10 | CGA 6 6 6 - CTG 4 3 3 | CCG 2 2 2 | CAG 2 2 2 | CGG 0 0 0 --------------------------------------------------------------------------- -Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT 9 9 9 | Ser AGT 2 2 2 - ATC 8 9 9 | ACC 8 8 8 | AAC 6 6 6 | AGC 3 3 3 - ATA 2 2 2 | ACA 5 5 5 | Lys AAA 18 18 18 | Arg AGA 6 6 6 -Met ATG 10 9 9 | ACG 1 1 1 | AAG 6 6 6 | AGG 1 1 1 --------------------------------------------------------------------------- -Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23 - GTC 1 1 1 | GCC 5 5 5 | GAC 5 6 6 | GGC 2 2 2 - GTA 13 13 13 | GCA 15 16 16 | Glu GAA 24 24 24 | GGA 13 13 13 - GTG 4 4 4 | GCG 1 0 0 | GAG 10 9 9 | GGG 9 9 9 --------------------------------------------------------------------------- - - -Sums --------------------------------------------------- -Phe TTT 126 | Ser TCT 53 | Tyr TAT 117 | Cys TGT 45 - TTC 72 | TCC 37 | TAC 36 | TGC 27 -Leu TTA 81 | TCA 9 | *** TAA 0 | *** TGA 0 - TTG 90 | TCG 9 | TAG 0 | Trp TGG 72 --------------------------------------------------- -Leu CTT 81 | Pro CCT 99 | His CAT 81 | Arg CGT 99 - CTC 0 | CCC 52 | CAC 45 | CGC 45 - CTA 84 | CCA 27 | Gln CAA 88 | CGA 54 - CTG 33 | CCG 18 | CAG 18 | CGG 0 --------------------------------------------------- -Ile ATT 92 | Thr ACT 152 | Asn AAT 81 | Ser AGT 16 - ATC 77 | ACC 72 | AAC 54 | AGC 27 - ATA 18 | ACA 47 | Lys AAA 162 | Arg AGA 54 -Met ATG 87 | ACG 9 | AAG 54 | AGG 9 --------------------------------------------------- -Val GTT 131 | Ala GCT 215 | Asp GAT 198 | Gly GGT 207 - GTC 9 | GCC 44 | GAC 51 | GGC 18 - GTA 115 | GCA 141 | Glu GAA 218 | GGA 117 - GTG 36 | GCG 1 | GAG 84 | GGG 81 --------------------------------------------------- - - - -(A) Nei-Gojobori (1986) method - - - -Nei & Gojobori 1986. dN/dS (dN, dS) -(Note: This matrix is not used in later ML. analysis. -Use runmode = -2 for ML pairwise comparison.) - -Pdel181_DNA2 -Pfre186_DNA2 -1.0000 (0.0009 0.0000) -Pgra187_DNA2 1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088) -Phet26_DNA21 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117) -Pmex37_DNA21 -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029) -Ptre197_DNA2 1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058) -WHR1_DNA225 0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117) -YALD273_DNA5 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088) -Pop_trich_ch 1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000) - - -(B) Yang & Nielsen (2000) method - -Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43 - -(equal weighting of pathways) - -seq. seq. S N t kappa omega dN +- SE dS +- SE - - 2 1 337.9 1087.1 0.0021 4.2358 99.0000 0.0009 +- 0.0009 -0.0000 +- 0.0000 - 3 1 335.1 1089.9 0.0276 4.2358 1.0246 0.0092 +- 0.0029 0.0090 +- 0.0052 - 3 2 334.8 1090.2 0.0297 4.2358 1.1268 0.0102 +- 0.0031 0.0090 +- 0.0052 - 4 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 - 4 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 - 4 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 - 5 1 338.1 1086.9 0.0106 4.2358 99.0000 0.0046 +- 0.0021 -0.0000 +- 0.0000 - 5 2 337.8 1087.2 0.0084 4.2358 99.0000 0.0037 +- 0.0018 -0.0000 +- 0.0000 - 5 3 335.0 1090.0 0.0254 4.2358 0.9214 0.0083 +- 0.0028 0.0090 +- 0.0052 - 5 4 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 - 6 1 334.8 1090.2 0.0254 4.2358 1.5397 0.0092 +- 0.0029 0.0060 +- 0.0042 - 6 2 334.5 1090.5 0.0276 4.2358 1.6932 0.0102 +- 0.0031 0.0060 +- 0.0042 - 6 3 331.7 1093.3 0.0064 4.2358 0.0000 -0.0000 +- 0.0000 0.0091 +- 0.0053 - 6 4 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 - 6 5 334.7 1090.3 0.0233 4.2358 1.3847 0.0083 +- 0.0028 0.0060 +- 0.0042 - 7 1 338.8 1086.2 0.0148 4.2358 0.7790 0.0046 +- 0.0021 0.0059 +- 0.0042 - 7 2 338.5 1086.5 0.0169 4.2358 0.9344 0.0055 +- 0.0023 0.0059 +- 0.0042 - 7 3 335.7 1089.3 0.0255 4.2358 0.4278 0.0065 +- 0.0024 0.0151 +- 0.0068 - 7 4 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 - 7 5 338.7 1086.3 0.0127 4.2358 0.6226 0.0037 +- 0.0018 0.0059 +- 0.0042 - 7 6 335.4 1089.6 0.0233 4.2358 0.5368 0.0065 +- 0.0024 0.0120 +- 0.0060 - 8 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 - 8 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 - 8 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 - 8 4 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 - 8 5 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 - 8 6 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 - 8 7 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 - 9 1 337.9 1087.1 0.0106 4.2358 1.2441 0.0037 +- 0.0018 0.0030 +- 0.0030 - 9 2 337.6 1087.4 0.0127 4.2358 1.5546 0.0046 +- 0.0021 0.0030 +- 0.0030 - 9 3 334.8 1090.2 0.0212 4.2358 0.4581 0.0055 +- 0.0023 0.0121 +- 0.0061 - 9 4 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 - 9 5 337.8 1087.2 0.0084 4.2358 0.9322 0.0028 +- 0.0016 0.0030 +- 0.0030 - 9 6 334.5 1090.5 0.0190 4.2358 0.6124 0.0055 +- 0.0023 0.0090 +- 0.0052 - 9 7 338.5 1086.5 0.0127 4.2358 0.3104 0.0028 +- 0.0016 0.0089 +- 0.0052 - 9 8 337.6 1087.4 -0.0000 4.2358 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000 - - -(C) LWL85, LPB93 & LWLm methods - -Li W.-H., C.-I. Wu, Luo (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174. -Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99 -Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes - rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281 -Yang Z (2006) Computational Molecular Evolution. Oxford University Press, Oxford. Eqs. 2.12 & 2.13 - -2 (Pfre186_DNA2) vs. 1 (Pdel181_DNA2) - -L(i): 923.0 268.5 233.5 sum= 1425.0 -Ns(i): 1.0000 0.0000 0.0000 sum= 1.0000 -Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 -A(i): 0.0011 0.0000 0.0000 -B(i): -0.0000 -0.0000 -0.0000 -LWL85: dS = 0.0000 dN = 0.0009 w = inf S = 323.0 N = 1102.0 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = 0.0000 dN = 0.0011 w = inf - -3 (Pgra187_DNA2) vs. 1 (Pdel181_DNA2) - -L(i): 923.0 269.0 233.0 sum= 1425.0 -Ns(i): 5.5000 1.5000 1.0000 sum= 8.0000 -Nv(i): 2.5000 2.5000 0.0000 sum= 5.0000 -A(i): 0.0060 0.0056 0.0043 -B(i): 0.0027 0.0094 -0.0000 -LWL85: dS = 0.0078 dN = 0.0096 w = 1.2280 S = 322.7 N = 1102.3 -LWL85m: dS = 0.0050 dN = 0.0115 w = 2.2818 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0102 w = 2.0369 - -3 (Pgra187_DNA2) vs. 2 (Pfre186_DNA2) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 6.5000 1.5000 1.0000 sum= 9.0000 -Nv(i): 2.5000 2.5000 0.0000 sum= 5.0000 -A(i): 0.0071 0.0056 0.0043 -B(i): 0.0027 0.0094 -0.0000 -LWL85: dS = 0.0078 dN = 0.0105 w = 1.3442 S = 322.3 N = 1102.7 -LWL85m: dS = 0.0050 dN = 0.0126 w = 2.5010 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0113 w = 2.2557 - -4 (Phet26_DNA21) vs. 1 (Pdel181_DNA2) - -L(i): 922.5 269.0 233.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 -LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 - -4 (Phet26_DNA21) vs. 2 (Pfre186_DNA2) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0027 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 - -4 (Phet26_DNA21) vs. 3 (Pgra187_DNA2) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): 0.0044 0.0037 0.0087 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 - -5 (Pmex37_DNA21) vs. 1 (Pdel181_DNA2) - -L(i): 923.0 269.0 233.0 sum= 1425.0 -Ns(i): 2.0000 0.0000 0.0000 sum= 2.0000 -Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 -A(i): 0.0022 -0.0000 0.0000 -B(i): 0.0022 0.0037 -0.0000 -LWL85: dS = -0.0000 dN = 0.0046 w =-1568.0041 S = 322.7 N = 1102.3 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = -0.0000 dN = 0.0047 w =-2519.1394 - -5 (Pmex37_DNA21) vs. 2 (Pfre186_DNA2) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 1.0000 0.0000 0.0000 sum= 1.0000 -Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 -A(i): 0.0011 -0.0000 0.0000 -B(i): 0.0022 0.0037 -0.0000 -LWL85: dS = -0.0000 dN = 0.0036 w =-1254.3509 S = 322.3 N = 1102.7 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = -0.0000 dN = 0.0036 w =-1938.1612 - -5 (Pmex37_DNA21) vs. 3 (Pgra187_DNA2) - -L(i): 923.0 270.0 232.0 sum= 1425.0 -Ns(i): 5.5000 1.5000 1.0000 sum= 8.0000 -Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 -A(i): 0.0060 0.0056 0.0043 -B(i): 0.0027 0.0056 -0.0000 -LWL85: dS = 0.0078 dN = 0.0087 w = 1.1081 S = 322.0 N = 1103.0 -LWL85m: dS = 0.0050 dN = 0.0104 w = 2.0644 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0094 w = 1.8682 - -5 (Pmex37_DNA21) vs. 4 (Phet26_DNA21) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 -0.0000 -0.0000 -LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 - -6 (Ptre197_DNA2) vs. 1 (Pdel181_DNA2) - -L(i): 923.0 269.0 233.0 sum= 1425.0 -Ns(i): 5.5000 0.5000 2.0000 sum= 8.0000 -Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 -A(i): 0.0060 0.0019 0.0087 -B(i): 0.0027 0.0056 -0.0000 -LWL85: dS = 0.0078 dN = 0.0087 w = 1.1111 S = 322.7 N = 1102.3 -LWL85m: dS = 0.0050 dN = 0.0104 w = 2.0645 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0094 w = 1.8688 - -6 (Ptre197_DNA2) vs. 2 (Pfre186_DNA2) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 6.5000 0.5000 2.0000 sum= 9.0000 -Nv(i): 2.5000 1.5000 0.0000 sum= 4.0000 -A(i): 0.0071 0.0019 0.0087 -B(i): 0.0027 0.0056 -0.0000 -LWL85: dS = 0.0078 dN = 0.0096 w = 1.2275 S = 322.3 N = 1102.7 -LWL85m: dS = 0.0050 dN = 0.0115 w = 2.2838 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0105 w = 2.0879 - -6 (Ptre197_DNA2) vs. 3 (Pgra187_DNA2) - -L(i): 923.0 270.0 232.0 sum= 1425.0 -Ns(i): 0.0000 1.0000 1.0000 sum= 2.0000 -Nv(i): 0.0000 1.0000 0.0000 sum= 1.0000 -A(i): 0.0000 0.0037 0.0043 -B(i): -0.0000 0.0037 -0.0000 -LWL85: dS = 0.0062 dN = 0.0009 w = 0.1457 S = 322.0 N = 1103.0 -LWL85m: dS = 0.0040 dN = 0.0011 w = 0.2715 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0040 dN = 0.0008 w = 0.2100 - -6 (Ptre197_DNA2) vs. 4 (Phet26_DNA21) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 -Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 -A(i): 0.0044 -0.0000 0.0131 -B(i): 0.0016 0.0019 -0.0000 -LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 - -6 (Ptre197_DNA2) vs. 5 (Pmex37_DNA21) - -L(i): 923.0 270.0 232.0 sum= 1425.0 -Ns(i): 5.5000 0.5000 2.0000 sum= 8.0000 -Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 -A(i): 0.0060 0.0019 0.0087 -B(i): 0.0027 0.0019 -0.0000 -LWL85: dS = 0.0078 dN = 0.0078 w = 0.9913 S = 322.0 N = 1103.0 -LWL85m: dS = 0.0050 dN = 0.0093 w = 1.8469 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0085 w = 1.6999 - -7 (WHR1_DNA225) vs. 1 (Pdel181_DNA2) - -L(i): 923.0 268.5 233.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 2.0000 sum= 4.0000 -Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 -A(i): 0.0016 0.0019 0.0086 -B(i): 0.0027 0.0019 -0.0000 -LWL85: dS = 0.0078 dN = 0.0041 w = 0.5251 S = 323.0 N = 1102.0 -LWL85m: dS = 0.0050 dN = 0.0049 w = 0.9743 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0042 w = 0.8280 - -7 (WHR1_DNA225) vs. 2 (Pfre186_DNA2) - -L(i): 923.0 269.0 233.0 sum= 1425.0 -Ns(i): 2.5000 0.5000 2.0000 sum= 5.0000 -Nv(i): 2.5000 0.5000 0.0000 sum= 3.0000 -A(i): 0.0027 0.0019 0.0087 -B(i): 0.0027 0.0019 -0.0000 -LWL85: dS = 0.0078 dN = 0.0050 w = 0.6414 S = 322.7 N = 1102.3 -LWL85m: dS = 0.0050 dN = 0.0060 w = 1.1918 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0052 w = 1.0452 - -7 (WHR1_DNA225) vs. 3 (Pgra187_DNA2) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 4.0000 1.0000 3.0000 sum= 8.0000 -Nv(i): 2.0000 2.0000 0.0000 sum= 4.0000 -A(i): 0.0044 0.0037 0.0131 -B(i): 0.0022 0.0075 -0.0000 -LWL85: dS = 0.0126 dN = 0.0073 w = 0.5811 S = 322.3 N = 1102.7 -LWL85m: dS = 0.0081 dN = 0.0087 w = 1.0811 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0081 dN = 0.0077 w = 0.9591 - -7 (WHR1_DNA225) vs. 4 (Phet26_DNA21) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): -0.0000 -0.0000 0.0130 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 - -7 (WHR1_DNA225) vs. 5 (Pmex37_DNA21) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 2.0000 sum= 4.0000 -Nv(i): 0.5000 1.5000 0.0000 sum= 2.0000 -A(i): 0.0016 0.0019 0.0087 -B(i): 0.0005 0.0056 -0.0000 -LWL85: dS = 0.0078 dN = 0.0032 w = 0.4075 S = 322.3 N = 1102.7 -LWL85m: dS = 0.0050 dN = 0.0038 w = 0.7582 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0050 dN = 0.0033 w = 0.6602 - -7 (WHR1_DNA225) vs. 6 (Ptre197_DNA2) - -L(i): 923.0 269.5 232.5 sum= 1425.0 -Ns(i): 4.0000 0.0000 4.0000 sum= 8.0000 -Nv(i): 2.0000 1.0000 0.0000 sum= 3.0000 -A(i): 0.0044 -0.0000 0.0175 -B(i): 0.0022 0.0037 -0.0000 -LWL85: dS = 0.0126 dN = 0.0064 w = 0.5052 S = 322.3 N = 1102.7 -LWL85m: dS = 0.0081 dN = 0.0076 w = 0.9400 S = 502.0 N = 923.0 (rho = 1.000) -LPB93: dS = 0.0081 dN = 0.0069 w = 0.8491 - -8 (YALD273_DNA5) vs. 1 (Pdel181_DNA2) - -L(i): 922.5 269.0 233.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 -LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 - -8 (YALD273_DNA5) vs. 2 (Pfre186_DNA2) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0027 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 - -8 (YALD273_DNA5) vs. 3 (Pgra187_DNA2) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): 0.0044 0.0037 0.0087 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 - -8 (YALD273_DNA5) vs. 4 (Phet26_DNA21) - -L(i): 922.0 270.0 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 -Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 -A(i): 0.0000 0.0000 0.0000 -B(i): -0.0000 -0.0000 -0.0000 -LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = 0.0000 dN = 0.0000 w = nan - -8 (YALD273_DNA5) vs. 5 (Pmex37_DNA21) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 -0.0000 -0.0000 -LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 - -8 (YALD273_DNA5) vs. 6 (Ptre197_DNA2) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 -Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 -A(i): 0.0044 -0.0000 0.0131 -B(i): 0.0016 0.0019 -0.0000 -LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 - -8 (YALD273_DNA5) vs. 7 (WHR1_DNA225) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): -0.0000 -0.0000 0.0130 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 - -9 (Pop_trich_ch) vs. 1 (Pdel181_DNA2) - -L(i): 922.5 269.0 233.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0032 w = 0.6832 S = 323.2 N = 1101.8 -LWL85m: dS = 0.0030 dN = 0.0038 w = 1.2689 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0033 w = 1.1052 - -9 (Pop_trich_ch) vs. 2 (Pfre186_DNA2) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 2.5000 0.5000 1.0000 sum= 4.0000 -Nv(i): 1.0000 1.0000 0.0000 sum= 2.0000 -A(i): 0.0027 0.0019 0.0043 -B(i): 0.0011 0.0037 -0.0000 -LWL85: dS = 0.0047 dN = 0.0041 w = 0.8779 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0030 dN = 0.0049 w = 1.6325 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0044 w = 1.4686 - -9 (Pop_trich_ch) vs. 3 (Pgra187_DNA2) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 1.0000 2.0000 sum= 7.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): 0.0044 0.0037 0.0087 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0064 w = 0.6803 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0076 w = 1.2668 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0069 w = 1.1440 - -9 (Pop_trich_ch) vs. 4 (Phet26_DNA21) - -L(i): 922.0 270.0 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 -Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 -A(i): 0.0000 0.0000 0.0000 -B(i): -0.0000 -0.0000 -0.0000 -LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = 0.0000 dN = 0.0000 w = nan - -9 (Pop_trich_ch) vs. 5 (Pmex37_DNA21) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 1.5000 0.5000 1.0000 sum= 3.0000 -Nv(i): 1.0000 0.0000 0.0000 sum= 1.0000 -A(i): 0.0016 0.0019 0.0043 -B(i): 0.0011 -0.0000 -0.0000 -LWL85: dS = 0.0047 dN = 0.0023 w = 0.4868 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0030 dN = 0.0027 w = 0.9065 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0030 dN = 0.0025 w = 0.8244 - -9 (Pop_trich_ch) vs. 6 (Ptre197_DNA2) - -L(i): 922.5 270.0 232.5 sum= 1425.0 -Ns(i): 4.0000 0.0000 3.0000 sum= 7.0000 -Nv(i): 1.5000 0.5000 0.0000 sum= 2.0000 -A(i): 0.0044 -0.0000 0.0131 -B(i): 0.0016 0.0019 -0.0000 -LWL85: dS = 0.0094 dN = 0.0055 w = 0.5801 S = 322.5 N = 1102.5 -LWL85m: dS = 0.0060 dN = 0.0065 w = 1.0802 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0060 w = 0.9989 - -9 (Pop_trich_ch) vs. 7 (WHR1_DNA225) - -L(i): 922.5 269.5 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 3.0000 sum= 3.0000 -Nv(i): 1.5000 1.5000 0.0000 sum= 3.0000 -A(i): -0.0000 -0.0000 0.0130 -B(i): 0.0016 0.0056 -0.0000 -LWL85: dS = 0.0094 dN = 0.0027 w = 0.2903 S = 322.8 N = 1102.2 -LWL85m: dS = 0.0060 dN = 0.0033 w = 0.5399 S = 502.5 N = 922.5 (rho = 1.000) -LPB93: dS = 0.0060 dN = 0.0025 w = 0.4178 - -9 (Pop_trich_ch) vs. 8 (YALD273_DNA5) - -L(i): 922.0 270.0 233.0 sum= 1425.0 -Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000 -Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000 -A(i): 0.0000 0.0000 0.0000 -B(i): -0.0000 -0.0000 -0.0000 -LWL85: dS = 0.0000 dN = 0.0000 w = nan S = 323.0 N = 1102.0 -LWL85m: dS = nan dN = nan w = nan S = nan N = nan (rho = nan) -LPB93: dS = 0.0000 dN = 0.0000 w = nan - -- 2.11.4.GIT