| 2010-01-22 |
jason | add an alphabet init arg and get/setter
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commit | commitdiff | tree |
| 2009-05-18 |
jason | requires the specific Loader instance to be 'use'ed
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commit | commitdiff | tree |
| 2009-05-15 |
jason | gene and exon are the proper SO even for tRNAs. Insure...
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commit | commitdiff | tree |
| 2009-04-02 |
jason | MPI output slightly different
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commit | commitdiff | tree |
| 2009-03-01 |
jason | simplify LD code a bit, we don't need to keep a running...
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commit | commitdiff | tree |
| 2009-02-05 |
jason | deal with empty intersection
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commit | commitdiff | tree |
| 2009-02-05 |
jason | handle some divide by zero problems
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commit | commitdiff | tree |
| 2009-02-05 |
jason | somre more total stats
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commit | commitdiff | tree |
| 2009-02-05 |
jason | remove MYISAM directives
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commit | commitdiff | tree |
| 2009-02-04 |
jason | I guess remove this, it breaks some things, although...
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commit | commitdiff | tree |
| 2008-12-16 |
jason | skip test count updated for instances when SVG::Graph...
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commit | commitdiff | tree |
| 2008-12-16 |
jason | parse DBlinks now supported
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commit | commitdiff | tree |
| 2008-12-16 |
jason | indentation and formatting only
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commit | commitdiff | tree |
| 2008-12-14 |
jason | another example BLAST
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commit | commitdiff | tree |
| 2008-12-06 |
jason | demonstrate with a valid 'site_model' as 'codons' rather...
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commit | commitdiff | tree |
| 2008-12-02 |
jason | XML::DOM dependancy
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commit | commitdiff | tree |
| 2008-10-28 |
jason | jasonfail. add missing test data file for FASTA v35.04
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commit | commitdiff | tree |
| 2008-10-23 |
jason | support new method in API get_seq_by_id
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commit | commitdiff | tree |
| 2008-10-23 |
jason | FASTA - 35.04 Parameters section parsing for Matrix
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commit | commitdiff | tree |
| 2008-10-23 |
jason | FASTA - 35.04 Parameters section parsing for Matrix
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commit | commitdiff | tree |
| 2008-10-22 |
jason | Allow multi-ID indexing per sequence. This can be rolled...
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commit | commitdiff | tree |
| 2008-10-22 |
jason | more specific warning
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commit | commitdiff | tree |
| 2008-10-22 |
jason | fix email address
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commit | commitdiff | tree |
| 2008-10-22 |
jason | fix email address
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commit | commitdiff | tree |
| 2008-09-16 |
jason | match '*' and '?' as well
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commit | commitdiff | tree |
| 2008-08-17 |
jason | fully implement Bio::LocationI
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commit | commitdiff | tree |
| 2008-06-19 |
jason | AAML parsing was failing on runmode=0 data (usertree)
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commit | commitdiff | tree |
| 2008-06-18 |
jason | avoid undefined warnings when start/end are empty....
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commit | commitdiff | tree |
| 2008-06-14 |
jason | set the ID, typo
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commit | commitdiff | tree |
| 2008-06-14 |
jason | More GFF3 like output
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commit | commitdiff | tree |
| 2008-06-14 |
jason | simplify list of special ID tags and their preferred...
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commit | commitdiff | tree |
| 2008-06-13 |
jason | doc expansion
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commit | commitdiff | tree |
| 2008-06-12 |
jason | some whitespace cleanup
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commit | commitdiff | tree |
| 2008-06-12 |
jason | inherit from Bio::Root::RootI instead of NodeI
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commit | commitdiff | tree |
| 2008-05-11 |
jason | first crack at a sort_hsps option in a Hit object,...
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commit | commitdiff | tree |
| 2008-05-11 |
jason | code simplification
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commit | commitdiff | tree |
| 2008-05-11 |
jason | bug #2492, credit to K.Thornton's implementation
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commit | commitdiff | tree |
| 2008-05-11 |
jason | bug 2492
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commit | commitdiff | tree |
| 2008-04-22 |
jason | bug #2491
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commit | commitdiff | tree |
| 2008-04-14 |
jason | typo
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commit | commitdiff | tree |
| 2008-03-19 |
jason | tag/value pairing associating with Trees
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commit | commitdiff | tree |
| 2008-03-19 |
jason | quiet some warnings on initialization
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commit | commitdiff | tree |
| 2008-03-12 |
jason | split sequence database into individual sequence files
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commit | commitdiff | tree |
| 2007-12-15 |
jason | Short circuit if the a1 is 0 to avoid divide by zero
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commit | commitdiff | tree |
| 2007-12-15 |
jason | some formatting -- committing before SVN merge
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commit | commitdiff | tree |
| 2007-12-03 |
jason | actually parse percent similar numbers out properly...
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commit | commitdiff | tree |
| 2007-11-27 |
jason | dependancies enumearated for Bio::PhyloNetwork
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commit | commitdiff | tree |
| 2007-11-27 |
jason | Initial commit of Phylogenetic Network code from Gabriel...
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commit | commitdiff | tree |
| 2007-11-27 |
jason | I'm pretty sure this returning correct values and tests...
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commit | commitdiff | tree |
| 2007-11-18 |
jason | add trailing newline
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commit | commitdiff | tree |
| 2007-11-06 |
jason | allow . in the names
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commit | commitdiff | tree |
| 2007-11-06 |
jason | Don't we need to include Bio::Tools::GFF
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commit | commitdiff | tree |
| 2007-11-01 |
jason | Parsing PAML4 and PAML3.15 should work now. Dealing...
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commit | commitdiff | tree |
| 2007-11-01 |
jason | add Codeml pairwise result for PAML4
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commit | commitdiff | tree |
| 2007-10-30 |
jason | Fixes from Claude Rispe and Fabrice Legeai for RST...
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commit | commitdiff | tree |
| 2007-10-26 |
jason | fix Genewise data moving and tests
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commit | commitdiff | tree |
| 2007-10-04 |
jason | force MYISAM for FULLTEXT indexed tables
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commit | commitdiff | tree |
| 2007-09-28 |
jason | allow -ID to be set on init
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commit | commitdiff | tree |
| 2007-09-26 |
jason | POD copy+paste fix
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commit | commitdiff | tree |
| 2007-09-17 |
jason | lowercase typo
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commit | commitdiff | tree |
| 2007-08-27 |
jason | return undef when demon is 0 for now in Tajima's D
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commit | commitdiff | tree |
| 2007-08-26 |
jason | for now let's report the offending codon in the message
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commit | commitdiff | tree |
| 2007-08-26 |
jason | some small code compaction in attempt to optimize,...
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commit | commitdiff | tree |
| 2007-08-26 |
jason | Fix some POD that was wrong. Test for completely missing...
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commit | commitdiff | tree |
| 2007-08-26 |
jason | Code optimization. Can skip ISA checking when building...
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commit | commitdiff | tree |
| 2007-08-26 |
jason | Code optimization. Can force a skip ISA checking for...
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commit | commitdiff | tree |
| 2007-08-26 |
jason | skip when we encounter gaps -- to better parameterize...
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commit | commitdiff | tree |
| 2007-08-20 |
jason | get the count right every time
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commit | commitdiff | tree |
| 2007-07-28 |
jason | don't force blankallele matching to be case insensitive...
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commit | commitdiff | tree |
| 2007-07-16 |
jason | move transcript score to transcript, set gene score...
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commit | commitdiff | tree |
| 2007-07-13 |
jason | unique_id not person_id
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commit | commitdiff | tree |
| 2007-07-13 |
jason | Add test for remove Individuals and allele freq
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commit | commitdiff | tree |
| 2007-07-06 |
jason | remove debugging
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commit | commitdiff | tree |
| 2007-07-06 |
jason | more FASTA-35 fixes, support multi-report files, parse...
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commit | commitdiff | tree |
| 2007-07-04 |
jason | minor reformatting
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commit | commitdiff | tree |
| 2007-07-04 |
jason | Changed API to used named parameters and only need...
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commit | commitdiff | tree |
| 2007-07-03 |
jason | FASTA-35 parsing tweak
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commit | commitdiff | tree |
| 2007-07-02 |
jason | McDonald-Kreitman implementation
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commit | commitdiff | tree |
| 2007-06-23 |
jason | use DEBUG instead of STDERR
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commit | commitdiff | tree |
| 2007-06-23 |
jason | refixed - now will get NHX bootstraps properly and...
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commit | commitdiff | tree |
| 2007-06-23 |
jason | deal with empty NHX fields as seen in NJTREE
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commit | commitdiff | tree |
| 2007-06-19 |
jason | this method needs to delegate to the db handle to get...
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commit | commitdiff | tree |
| 2007-06-18 |
jason | Converted to Test::More
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commit | commitdiff | tree |
| 2007-06-14 |
jason | add $
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commit | commitdiff | tree |
| 2007-06-14 |
jason | Added support for printing bootstrap values
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commit | commitdiff | tree |
| 2007-05-29 |
jason | don't need to guess the alphabet if we already know it
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commit | commitdiff | tree |
| 2007-05-29 |
jason | revert ... my mistake
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commit | commitdiff | tree |
| 2007-05-29 |
jason | POD fix in SYNOPSIS
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commit | commitdiff | tree |
| 2007-05-12 |
jason | TreeIO magic to now automatically move bootstrap values...
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commit | commitdiff | tree |
| 2007-05-12 |
jason | test for method to move bootstrap values from id values...
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commit | commitdiff | tree |
| 2007-05-12 |
jason | method to move bootstrap values from id values for...
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commit | commitdiff | tree |
| 2007-04-26 |
jason | whoops, I made a bug, test if we are in Result before...
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commit | commitdiff | tree |
| 2007-04-22 |
jason | Handle reports with no ending stanza
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commit | commitdiff | tree |
| 2007-04-22 |
jason | move some cached-handler code over from blast to help...
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commit | commitdiff | tree |
| 2007-04-17 |
jason | special MrBayes macro case, cleanup err msg a little...
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commit | commitdiff | tree |
| 2007-04-13 |
jason | some error checking
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commit | commitdiff | tree |
| 2007-04-13 |
jason | do not need to include Root.pm
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commit | commitdiff | tree |
| 2007-03-19 |
jason | correct package name in POD, use the seqname parsed...
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commit | commitdiff | tree |
| 2007-03-01 |
jason | bug #2220
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commit | commitdiff | tree |
| 2007-02-06 |
jason | remove errant reference to ENV variable in POD - this...
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commit | commitdiff | tree |
