fix hit count to go with database change, tests pass with BLAST+ 2.2.25+

[bioperl-run.git] / MANIFEST

AUTHORS
Build.PL
Changes
DEPENDENCIES
INSTALL
INSTALL.PROGRAMS
INSTALL.SKIP
lib/Bio/DB/ESoap.pm
lib/Bio/DB/ESoap/WSDL.pm
lib/Bio/DB/SoapEUtilities.pm
lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm
lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm
lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm
lib/Bio/DB/SoapEUtilities/Result.pm
lib/Bio/Factory/EMBOSS.pm
lib/Bio/Installer/Clustalw.pm
lib/Bio/Installer/EMBOSS.pm
lib/Bio/Installer/Generic.pm
lib/Bio/Installer/Hyphy.pm
lib/Bio/Installer/Muscle.pm
lib/Bio/Installer/PAML.pm
lib/Bio/Installer/Probcons.pm
lib/Bio/Installer/SLR.pm
lib/Bio/Installer/TCoffee.pm
lib/Bio/Tools/Run/Alignment/Amap.pm
lib/Bio/Tools/Run/Alignment/Blat.pm
lib/Bio/Tools/Run/Alignment/Clustalw.pm
lib/Bio/Tools/Run/Alignment/DBA.pm
lib/Bio/Tools/Run/Alignment/Exonerate.pm
lib/Bio/Tools/Run/Alignment/Gmap.pm
lib/Bio/Tools/Run/Alignment/Kalign.pm
lib/Bio/Tools/Run/Alignment/Lagan.pm
lib/Bio/Tools/Run/Alignment/MAFFT.pm
lib/Bio/Tools/Run/Alignment/Muscle.pm
lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
lib/Bio/Tools/Run/Alignment/Probalign.pm
lib/Bio/Tools/Run/Alignment/Probcons.pm
lib/Bio/Tools/Run/Alignment/Proda.pm
lib/Bio/Tools/Run/Alignment/Sim4.pm
lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
lib/Bio/Tools/Run/Alignment/TCoffee.pm
lib/Bio/Tools/Run/Analysis.pm
lib/Bio/Tools/Run/Analysis/soap.pm
lib/Bio/Tools/Run/AnalysisFactory.pm
lib/Bio/Tools/Run/AnalysisFactory/soap.pm
lib/Bio/Tools/Run/AssemblerBase.pm
lib/Bio/Tools/Run/BEDTools.pm
lib/Bio/Tools/Run/BEDTools/Config.pm
lib/Bio/Tools/Run/BlastPlus.pm
lib/Bio/Tools/Run/BlastPlus/Config.pm
lib/Bio/Tools/Run/Bowtie.pm
lib/Bio/Tools/Run/Bowtie/Config.pm
lib/Bio/Tools/Run/BWA.pm
lib/Bio/Tools/Run/BWA/Config.pm
lib/Bio/Tools/Run/Cap3.pm
lib/Bio/Tools/Run/Coil.pm
lib/Bio/Tools/Run/EMBOSSacd.pm
lib/Bio/Tools/Run/EMBOSSApplication.pm
lib/Bio/Tools/Run/Ensembl.pm
lib/Bio/Tools/Run/Eponine.pm
lib/Bio/Tools/Run/ERPIN.pm
lib/Bio/Tools/Run/FootPrinter.pm
lib/Bio/Tools/Run/Genemark.pm
lib/Bio/Tools/Run/Genewise.pm
lib/Bio/Tools/Run/Genscan.pm
lib/Bio/Tools/Run/Glimmer.pm
lib/Bio/Tools/Run/Hmmer.pm
lib/Bio/Tools/Run/Infernal.pm
lib/Bio/Tools/Run/Maq.pm
lib/Bio/Tools/Run/Maq/Config.pm
lib/Bio/Tools/Run/Match.pm
lib/Bio/Tools/Run/MCS.pm
lib/Bio/Tools/Run/Mdust.pm
lib/Bio/Tools/Run/Meme.pm
lib/Bio/Tools/Run/Minimo.pm
lib/Bio/Tools/Run/Newbler.pm
lib/Bio/Tools/Run/Phrap.pm
lib/Bio/Tools/Run/Phylo/Gerp.pm
lib/Bio/Tools/Run/Phylo/Gumby.pm
lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
lib/Bio/Tools/Run/Phylo/LVB.pm
lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
lib/Bio/Tools/Run/Phylo/PhyloBase.pm
lib/Bio/Tools/Run/Phylo/Phyml.pm
lib/Bio/Tools/Run/Phylo/QuickTree.pm
lib/Bio/Tools/Run/Phylo/Semphy.pm
lib/Bio/Tools/Run/Phylo/SLR.pm
lib/Bio/Tools/Run/Primate.pm
lib/Bio/Tools/Run/Primer3.pm
lib/Bio/Tools/Run/Prints.pm
lib/Bio/Tools/Run/Profile.pm
lib/Bio/Tools/Run/Promoterwise.pm
lib/Bio/Tools/Run/Pseudowise.pm
lib/Bio/Tools/Run/RepeatMasker.pm
lib/Bio/Tools/Run/RNAMotif.pm
lib/Bio/Tools/Run/Samtools.pm
lib/Bio/Tools/Run/Samtools/Config.pm
lib/Bio/Tools/Run/Seg.pm
lib/Bio/Tools/Run/Signalp.pm
lib/Bio/Tools/Run/Simprot.pm
lib/Bio/Tools/Run/StandAloneBlastPlus.pm
lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
lib/Bio/Tools/Run/TigrAssembler.pm
lib/Bio/Tools/Run/Tmhmm.pm
lib/Bio/Tools/Run/TribeMCL.pm
lib/Bio/Tools/Run/tRNAscanSE.pm
lib/Bio/Tools/Run/Vista.pm
LICENSE
MANIFEST                        This list of files
README
scripts/bioperl_application_installer.PLS
scripts/multi_hmmsearch.PLS
scripts/panalysis.PLS
scripts/papplmaker.PLS
scripts/run_neighbor.PLS
scripts/run_protdist.PLS
t/Amap.t
t/Analysis_soap.t
t/AnalysisFactory_soap.t
t/BEDTools.t
t/Blat.t
t/Bowtie.t
t/BWA.t
t/Cap3.t
t/Clustalw.t
t/Coil.t
t/Consense.t
t/data/219877.cdna.fasta
t/data/219877.tree
t/data/277523.cdna.fasta
t/data/277523.tree
t/data/amino.fa
t/data/apes.multi_fasta
t/data/apes.newick
t/data/blat_dna.fa
t/data/bowtie/indexes/e_coli.1.ebwt
t/data/bowtie/indexes/e_coli.2.ebwt
t/data/bowtie/indexes/e_coli.3.ebwt
t/data/bowtie/indexes/e_coli.4.ebwt
t/data/bowtie/indexes/e_coli.rev.1.ebwt
t/data/bowtie/indexes/e_coli.rev.2.ebwt
t/data/bowtie/reads/e_coli.cb
t/data/bowtie/reads/e_coli_1000.fa
t/data/bowtie/reads/e_coli_1000.fq
t/data/bowtie/reads/e_coli_1000.raw
t/data/bowtie/reads/e_coli_10000snp.fa
t/data/bowtie/reads/e_coli_10000snp.fq
t/data/bowtie/reads/e_coli_1000_1.fa
t/data/bowtie/reads/e_coli_1000_1.fq
t/data/bowtie/reads/e_coli_1000_2.fa
t/data/bowtie/reads/e_coli_1000_2.fq
t/data/campycoli.fas
t/data/cel-cbr-fam.aln
t/data/codeml.mlc
t/data/coil_protein_input
t/data/consense.treefile
t/data/consensus.cns
t/data/cysprot.fa
t/data/cysprot.msf
t/data/cysprot.raxml.tre
t/data/cysprot.stockholm
t/data/cysprot1a.fa
t/data/cysprot1a.msf
t/data/cysprot1b.fa
t/data/cysprot1b.msf
t/data/dba1a.fa
t/data/dba1b.fa
t/data/dba2.fa
t/data/dna1.fa
t/data/dna2.fa
t/data/dna_seqs1.phy
t/data/e_coli.bed3
t/data/e_coli_1.bedpe
t/data/e_coli_2.bedpe
t/data/ecolitst.fa
t/data/efetch_seq.wsdl
t/data/elink_result.xml
t/data/eponine.fa
t/data/esearch_result.xml
t/data/esum_result.xml
t/data/eutils.wsdl
t/data/exonerate_cdna.fa
t/data/exonerate_cdna_rev.fa
t/data/exonerate_genomic.fa
t/data/exonerate_genomic_rev.fa
t/data/fasta.fa
t/data/fastalib.fa
t/data/fastaprot.fa
t/data/fontfile
t/data/FootPrinter.seq.fa
t/data/Ft.bam
t/data/Ft.bed
t/data/Ft.frag.fas
t/data/gb_result.xml
t/data/Genscan.FastA
t/data/gerp/ENr111.gerp.tree
t/data/gerp/ENr111.mfa.gz
t/data/gf-s85.phylip
t/data/gumby/hmrd.mfa
t/data/gumby/hmrd.tree
t/data/gumby/human.gff
t/data/gumby/readme.txt
t/data/H_pylori_J99.fasta
t/data/H_pylori_J99.glimmer2.icm
t/data/H_pylori_J99.glimmer3.icm
t/data/her2-edited.fasta
t/data/hmmpfam_protein_input
t/data/human.genomic
t/data/hyphy1.fasta
t/data/hyphy1.tree
t/data/lagan_dna.fa
t/data/longnames.aln
t/data/lvb.fa
t/data/lvb_sequential.phy
t/data/neighbor.dist
t/data/new_dna.fa
t/data/new_pep.fa
t/data/njtree_aln2.nucl.mfa
t/data/NM_002254.gb
t/data/NM_002254.tfa
t/data/pal2nal.aln
t/data/pal2nal.nuc
t/data/pfam_sample_R11
t/data/Phrap.fa
t/data/primate_query.fa
t/data/primate_target.fa
t/data/Primer3.fa
t/data/prints.dat
t/data/Prints_prot.FastA
t/data/profile_prot.FastA
t/data/prosite.dat
t/data/protpars.phy
t/data/ps1.fa
t/data/purine.1.sto
t/data/purine.added.fa
t/data/purine.all.fa
t/data/purine.c.cm
t/data/purine.cm
t/data/r1.fq
t/data/r1bwa.fq
t/data/r2.fq
t/data/r2bwa.fq
t/data/repeatmasker.fa
t/data/road.pep
t/data/sample_dataset_1.fa
t/data/sample_dataset_1.qual
t/data/segmask_data.asn
t/data/semphy.seq
t/data/semphy.tree
t/data/signalp_input_protein
t/data/sim4_cdna.fa
t/data/sim4_database.fa
t/data/sim4_genomic.fa
t/data/simprot_tree.nh
t/data/species_tree_njtree.nh
t/data/taxdump/names.dmp
t/data/taxdump/nodes.dmp
t/data/test-aln.msf
t/data/test-query.fas
t/data/test-spa-p.fas
t/data/test-spa.fas
t/data/test.txt
t/data/test_prot.FastA
t/data/transfac.dat
t/data/tree_of_life
t/data/treefile.example
t/data/TribeMCL.bls
t/data/TribeMCL.desc
t/data/vista.cls
t/data/vista.gff
t/data/xprt.gb
t/DBA.t
t/DrawGram.t
t/DrawTree.t
t/EMBOSS.t
t/Ensembl.t
t/Eponine.t
t/Exonerate.t
t/FootPrinter.t
t/Genemark.hmm.prokaryotic.t
t/Genewise.t
t/Genscan.t
t/Gerp.t
t/Glimmer2.t
t/Glimmer3.t
t/gmap-run.t
t/Gumby.t
t/Hmmer.t
t/Hyphy.t
t/Infernal.t
t/Kalign.t
t/Lagan.t
t/lib/Sub/Uplevel.pm
t/lib/Test/Builder.pm
t/lib/Test/Builder/Module.pm
t/lib/Test/Builder/Tester.pm
t/lib/Test/Exception.pm
t/lib/Test/Harness.pm
t/lib/Test/Harness/Assert.pm
t/lib/Test/Harness/Iterator.pm
t/lib/Test/Harness/Point.pm
t/lib/Test/Harness/Results.pm
t/lib/Test/Harness/Straps.pm
t/lib/Test/Harness/TAP.pod
t/lib/Test/Harness/Util.pm
t/lib/Test/More.pm
t/lib/Test/Simple.pm
t/lib/Test/Tutorial.pod
t/lib/Test/Warn.pm
t/LVB.t
t/MAFFT.t
t/Maq.t
t/Match.t
t/MCS.t
t/Mdust.t
t/Meme.t
t/Minimo.t
t/Molphy.t
t/Muscle.t
t/Neighbor.t
t/Newbler.t
t/Njtree.t
t/Pal2Nal.t
t/PAML.t
t/PhastCons.t
t/Phrap.t
t/Phyml.t
t/Primate.t
t/Primer3.t
t/Prints.t
t/Probalign.t
t/Probcons.t
t/Profile.t
t/Promoterwise.t
t/ProtDist.t
t/ProtPars.t
t/Pseudowise.t
t/QuickTree.t
t/RepeatMasker.t
t/SABlastPlus.t
t/Samtools.t
t/Seg.t
t/Semphy.t
t/SeqBoot.t
t/Signalp.t
t/Sim4.t
t/Simprot.t
t/SLR.t
t/SoapEU-function.t
t/SoapEU-unit.t
t/StandAloneFasta.t
t/TCoffee.t
t/TigrAssembler.t
t/Tmhmm.t
t/TribeMCL.t
t/tRNAscanSE.t
t/Vista.t