[med-svn] [bioperl] 02/06: New upstream version 1.7.2
Andreas Tille
tille at debian.org
Sun Dec 3 18:00:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bioperl.
commit 469af4729c31539afdac12dadb4cee706157b827
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 18:52:42 2017 +0100
New upstream version 1.7.2
---
.travis.yml | 81 +-
Bio/AlignIO/phylip.pm | 529 +++---
Bio/AlignIO/xmfa.pm | 30 +-
Bio/AnalysisI.pm | 2 +-
Bio/Annotation/OntologyTerm.pm | 2 +-
Bio/AnnotationCollectionI.pm | 2 +-
Bio/Assembly/Contig.pm | 40 +-
Bio/Assembly/ScaffoldI.pm | 2 +-
Bio/Assembly/Singlet.pm | 2 +-
Bio/Assembly/Tools/ContigSpectrum.pm | 2 +-
Bio/Cluster/UniGene.pm | 4 +-
Bio/DB/EMBL.pm | 2 +-
Bio/DB/Fasta.pm | 2 +-
Bio/DB/Flat/BinarySearch.pm | 2 +-
Bio/DB/GFF.pm | 6 +-
Bio/DB/GFF/Adaptor/dbi.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysql.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/oracle.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/pg.pm | 2 +-
Bio/DB/GFF/Segment.pm | 6 +-
Bio/DB/GenBank.pm | 2 +-
Bio/DB/GenPept.pm | 2 +-
Bio/DB/GenericWebAgent.pm | 24 +-
Bio/DB/HIV/HIVQueryHelper.pm | 2 +-
Bio/DB/IndexedBase.pm | 78 +-
Bio/DB/LocationI.pm | 20 +-
Bio/DB/MeSH.pm | 4 +-
Bio/DB/Qual.pm | 2 +-
Bio/DB/Query/HIVQuery.pm | 2 +-
Bio/DB/RefSeq.pm | 4 +-
Bio/DB/ReferenceI.pm | 20 +-
Bio/DB/Registry.pm | 38 +-
Bio/DB/SeqFeature/Store.pm | 2 +-
Bio/DB/SeqFeature/Store/DBI/SQLite.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF2Loader.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF3Loader.pm | 6 +-
Bio/DB/SeqFeature/Store/Loader.pm | 2 +-
Bio/DB/TFBS/transfac_pro.pm | 8 +-
Bio/DB/Taxonomy/entrez.pm | 122 +-
Bio/DB/Taxonomy/flatfile.pm | 2 +-
Bio/DB/Taxonomy/sqlite.pm | 6 +-
Bio/DB/WebDBSeqI.pm | 4 +-
Bio/DescribableI.pm | 2 +-
Bio/Factory/ApplicationFactoryI.pm | 12 +-
Bio/Factory/ObjectFactoryI.pm | 2 +-
Bio/Index/Abstract.pm | 68 +-
Bio/Index/AbstractSeq.pm | 2 +-
Bio/Index/Blast.pm | 60 +-
Bio/Index/BlastTable.pm | 52 +-
Bio/Index/Hmmer.pm | 54 +-
Bio/Index/Stockholm.pm | 6 +-
Bio/LiveSeq/IO/Loader.pm | 2 +-
Bio/LiveSeq/IO/README | 2 +-
Bio/LiveSeq/Mutation.pm | 2 +-
Bio/LiveSeq/SeqI.pm | 4 +-
Bio/LocatableSeq.pm | 2 +-
Bio/Location/Atomic.pm | 10 +-
Bio/Location/Fuzzy.pm | 2 +-
Bio/Location/FuzzyLocationI.pm | 2 +-
Bio/Location/Simple.pm | 6 +-
Bio/Location/Split.pm | 2 +-
Bio/Location/SplitLocationI.pm | 2 +-
Bio/LocationI.pm | 2 +-
Bio/Map/CytoMarker.pm | 2 +-
Bio/Map/CytoPosition.pm | 6 +-
Bio/Map/GeneRelative.pm | 4 +-
Bio/Map/Microsatellite.pm | 2 +-
Bio/Map/OrderedPosition.pm | 2 +-
Bio/Map/Physical.pm | 2 +-
Bio/Map/Position.pm | 2 +-
Bio/Map/PositionI.pm | 2 +-
Bio/Map/Relative.pm | 2 +-
Bio/Map/TranscriptionFactor.pm | 2 +-
Bio/Matrix/Generic.pm | 6 +-
Bio/Matrix/PSM/IO.pm | 2 +-
Bio/Matrix/PSM/IO/masta.pm | 6 +-
Bio/Matrix/PSM/InstanceSite.pm | 2 +-
Bio/Matrix/PSM/ProtMatrix.pm | 6 +-
Bio/Matrix/PSM/ProtPsm.pm | 2 +-
Bio/Matrix/PSM/Psm.pm | 4 +-
Bio/Matrix/PSM/PsmI.pm | 4 +-
Bio/Matrix/PSM/SiteMatrix.pm | 12 +-
Bio/Matrix/PSM/SiteMatrixI.pm | 4 +-
Bio/Ontology/OntologyStore.pm | 2 +-
Bio/Ontology/SimpleOntologyEngine.pm | 2 +-
Bio/Ontology/Term.pm | 4 +-
Bio/Ontology/TermI.pm | 2 +-
Bio/OntologyIO/Handlers/BaseSAXHandler.pm | 26 +-
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm | 4 +-
Bio/OntologyIO/obo.pm | 22 +-
Bio/ParameterBaseI.pm | 22 +-
Bio/Perl.pm | 2 +-
Bio/PopGen/HtSNP.pm | 6 +-
Bio/PopGen/Individual.pm | 2 +-
Bio/PopGen/Population.pm | 4 +-
Bio/PopGen/TagHaplotype.pm | 4 +-
Bio/PrimarySeq.pm | 10 +-
Bio/PrimarySeqI.pm | 8 +-
Bio/PullParserI.pm | 2 +-
Bio/Restriction/Analysis.pm | 2 +-
Bio/Restriction/Enzyme.pm | 2 +-
Bio/Restriction/EnzymeI.pm | 2 +-
Bio/Restriction/IO/base.pm | 6 +-
Bio/Restriction/IO/itype2.pm | 2 +-
Bio/Root/Exception.pm | 2 +-
Bio/Root/Root.pm | 2 +-
Bio/Root/Storable.pm | 4 +-
Bio/Root/Test.pm | 6 +-
Bio/Root/Utilities.pm | 10 +-
Bio/Root/Version.pm | 2 +-
Bio/Search/BlastUtils.pm | 2 +-
Bio/Search/HSP/BlastPullHSP.pm | 2 +-
Bio/Search/HSP/GenericHSP.pm | 2 +-
Bio/Search/HSP/HMMERHSP.pm | 2 +-
Bio/Search/HSP/HSPI.pm | 2 +-
Bio/Search/HSP/ModelHSP.pm | 2 +-
Bio/Search/HSP/PullHSPI.pm | 2 +-
Bio/Search/Hit/GenericHit.pm | 2 +-
Bio/Search/Hit/HMMERHit.pm | 2 +-
Bio/Search/Hit/ModelHit.pm | 2 +-
Bio/Search/Iteration/IterationI.pm | 2 +-
Bio/Search/SearchUtils.pm | 2 +-
Bio/Search/Tiling/TilingI.pm | 2 +-
Bio/SearchDist.pm | 2 +-
Bio/SearchIO.pm | 58 +-
Bio/SearchIO/Writer/HTMLResultWriter.pm | 2 +-
Bio/SearchIO/Writer/TextResultWriter.pm | 2 +-
Bio/SearchIO/exonerate.pm | 2 +-
Bio/SearchIO/fasta.pm | 48 +-
Bio/SearchIO/hmmer3.pm | 2 +-
Bio/Seq.pm | 6 +-
Bio/Seq/EncodedSeq.pm | 2 +-
Bio/Seq/Meta/Array.pm | 4 +-
Bio/Seq/MetaI.pm | 8 +-
Bio/Seq/PrimaryQual.pm | 4 +-
Bio/Seq/PrimedSeq.pm | 2 +-
Bio/Seq/QualI.pm | 8 +-
Bio/Seq/RichSeqI.pm | 2 +-
Bio/Seq/SeqBuilder.pm | 4 +-
Bio/Seq/SeqWithQuality.pm | 14 +-
Bio/Seq/SequenceTrace.pm | 6 +-
Bio/Seq/SimulatedRead.pm | 2 +-
Bio/SeqFeature/AnnotationAdaptor.pm | 46 +-
Bio/SeqFeature/Computation.pm | 6 +-
Bio/SeqFeature/Generic.pm | 4 +-
Bio/SeqFeature/Lite.pm | 2 +-
Bio/SeqFeature/PositionProxy.pm | 2 +-
Bio/SeqFeature/SubSeq.pm | 2 +-
Bio/SeqFeature/Tools/Unflattener.pm | 2 +-
Bio/SeqFeature/TypedSeqFeatureI.pm | 2 +-
Bio/SeqIO.pm | 24 +-
Bio/SeqIO/ace.pm | 2 +-
Bio/SeqIO/bsml.pm | 20 +-
Bio/SeqIO/chadoxml.pm | 4 +-
Bio/SeqIO/chaos.pm | 2 +-
Bio/SeqIO/embl.pm | 6 +-
Bio/SeqIO/fasta.pm | 2 +-
Bio/SeqIO/fastq.pm | 2 +-
Bio/SeqIO/game/gameHandler.pm | 2 +-
Bio/SeqIO/gcg.pm | 4 +-
Bio/SeqIO/genbank.pm | 12 +-
Bio/SeqIO/interpro.pm | 2 +-
Bio/SeqIO/lasergene.pm | 2 +-
Bio/SeqIO/mbsout.pm | 2 +-
Bio/SeqIO/msout.pm | 2 +-
Bio/SeqIO/pir.pm | 59 +-
Bio/SeqIO/seqxml.pm | 2 +-
Bio/SeqIO/swiss.pm | 4 +-
Bio/SeqIO/tigr.pm | 4 +-
Bio/SeqUtils.pm | 2 +-
Bio/Structure/Entry.pm | 4 +-
Bio/Structure/Residue.pm | 4 +-
Bio/Structure/SecStr/DSSP/Res.pm | 8 +-
Bio/Structure/SecStr/STRIDE/Res.pm | 2 +-
Bio/Taxonomy.pm | 4 +-
Bio/Tools/AlignFactory.pm | 26 +-
Bio/Tools/Analysis/DNA/ESEfinder.pm | 2 +-
Bio/Tools/Analysis/Protein/ELM.pm | 2 +-
Bio/Tools/Analysis/Protein/NetPhos.pm | 4 +-
Bio/Tools/ECnumber.pm | 2 +-
Bio/Tools/GFF.pm | 140 +-
Bio/Tools/Phylo/Gerp.pm | 2 +-
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 -------------
Bio/Tools/PrositeScan.pm | 49 +-
Bio/Tools/SiRNA.pm | 2 +-
Bio/Tools/Sigcleave.pm | 2 +-
Bio/Tools/dpAlign.pm | 2 +-
Bio/Tools/pSW.pm | 4 +-
Bio/Tree/AlleleNode.pm | 2 +-
Bio/Tree/NodeI.pm | 2 +-
Bio/Tree/TreeFunctionsI.pm | 6 +-
Bio/TreeIO/nexus.pm | 2 +-
Bio/TreeIO/pag.pm | 2 +-
Bio/Variation/AAReverseMutate.pm | 2 +-
Bio/Variation/VariantI.pm | 6 +-
Changes | 21 +
DEPENDENCIES | 361 ++--
INSTALL.md | 81 +-
MANIFEST | 39 +-
META.json | 1619 +++++++++--------
META.yml | 1615 +++++++++--------
deobfuscator/Deobfuscator/bin/deob_index.pl | 30 +-
deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi | 2 +-
deobfuscator/Deobfuscator/cgi-bin/deob_help.html | 4 +-
.../Deobfuscator/cgi-bin/deob_interface.cgi | 4 +-
deobfuscator/Deobfuscator/lib/Deobfuscator.pm | 28 +-
examples/searchio/blast_example.pl | 4 +-
scripts/DB/bp_flanks.pl | 2 +-
scripts/index/bp_fetch.pl | 6 +-
scripts/index/bp_index.pl | 4 +-
scripts/seq/bp_seqcut.pl | 2 +-
scripts/seq/bp_unflatten_seq.pl | 2 +-
scripts/utilities/bp_netinstall.pl | 2 +-
scripts/utilities/bp_pairwise_kaks.pl | 211 ---
scripts/utilities/bp_search2gff.pl | 2 +-
t/LocalDB/Flat.t | 11 +-
t/RemoteDB/SeqVersion.t | 2 +-
t/RemoteDB/Taxonomy.t | 49 +-
t/SeqIO/pir.t | 48 +-
t/Tools/Phylo/PAML.t | 545 ------
t/Tools/PrositeScan.t | 44 +
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/ps_scan/out.PrositeScan | 10 +
t/data/seqfile-no-desc.pir | 9 +
t/data/singleNSsite.mlc | 152 --
t/data/testaln.xmfa | 14 +-
t/data/yn00.mlc | 106 --
t/data/yn00_45.mlc | 595 -------
travis_scripts/trigger-dockerhub.sh | 5 +
259 files changed, 3305 insertions(+), 12995 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index 0979812..55d65a3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,13 +1,32 @@
language: perl
perl:
+ - "5.26"
- "5.24"
- "5.20"
- "5.18"
- "5.16"
- - "5.14"
+
+matrix:
+ include:
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=1
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=2
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=3
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=4
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=5
+ - perl: 5.18
+ env: COVERAGE=1 TEST_PARTITION=6
sudo: false
-env: PERL_CPANM_OPT="--notest --force --skip-satisfied"
+env:
+ global:
+ - PERL_CPANM_OPT="--notest --force --skip-satisfied"
+ - BIOPERL_NETWORK_TESTING=0 # disables the network tests
+ - TEST_PARTITIONS=6
addons:
apt:
@@ -17,37 +36,38 @@ addons:
- libgd2-xpm-dev
- libxml2-dev
+before_install:
+ - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
+ - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
+ - source ~/travis-perl-helpers/init
+ - build-perl
+ - perl -V
+ - cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1
+ - cpanm Test::Pod 2>&1 | tail -n 1
+ - cpanm Bio::ASN1::EntrezGene 2>&1 | tail -n 1
+ - if [ "$TRAVIS_EVENT_TYPE" = "cron" -a "$BRANCH" = "network-cron-master" ]; then
+ export BIOPERL_NETWORK_TESTING=1;
+ git fetch origin master:master; git checkout master;
+ fi
+ - if [ "$BIOPERL_NETWORK_TESTING" = "1" ]; then
+ export TRAVIS_AUTHOR_TESTING=1;
+ export TRAVIS_RELEASE_TESTING=1;
+ cpanm LWP::UserAgent LWP::Protocol::https 2>&1 | tail -n 1;
+ fi
+ - build-dist
+ - cd $BUILD_DIR
install:
- #These are recommended or required Perl libraries:
- - "cpanm GD 2>&1 CGI | tail -n 1"
- - "cpanm HTML::TableExtract DBI Data::Stag DB_File 2>&1 | tail -n 1"
- - "cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1"
- - "cpanm Algorithm::Munkres Array::Compare Convert::Binary::C Error 2>&1 | tail -n 1"
- - "cpanm Graph SVG SVG::Graph GraphViz 2>&1 | tail -n 1"
- - "cpanm XML::DOM::XPath XML::Parser XML::Parser::PerlSAX 2>&1 | tail -n 1"
- - "cpanm XML::SAX XML::SAX::Writer XML::Simple XML::LibXML XML::Twig XML::Writer 2>&1 | tail -n 1"
- - "cpanm PostScript::TextBlock Set::Scalar Sort::Naturally YAML | tail -n 1"
- - "cpanm Math::Random Spreadsheet::ParseExcel | tail -n 1"
- - "cpanm Bio::Phylo | tail -n 1"
- - "cpanm Test::Weaken | tail -n 1"
- - "cpanm Test::Memory::Cycle | tail -n 1"
- #Test coverage from Coveralls
- #- cpanm --quiet --notest Devel::Cover::Report::Coveralls
- #for some reason tests and deps aren't skipped here. Will have to look into it more...
- #git repos, seems to only work for simple checkouts, so pure perl only (TODO: look into before_script for more detail)
- #- "git clone https://github.com/bioperl/Bio-Root.git; export PERL5LIB=$( pwd )/Bio-Root/lib:$PERL5LIB"
- #This installs BioPerl itself:
- - "perl ./Build.PL --accept"
-
+ - cpan-install --deps
+ - cpan-install --coverage
+before_script:
+ - coverage-setup
script:
- - "./Build test"
- #Devel::Cover coverage options are: statement, branch, condition, path, subroutine, pod, time, all and none
- #- "./Build build && cover -test -report coveralls" #complete version coverage test
- #- PERL5OPT=-MDevel::Cover=+ignore,prove,-coverage,statement,subroutine prove -lr t #limited version coverage test
- #- cover -report coveralls
-
+ - export AUTHOR_TESTING=${TRAVIS_AUTHOR_TESTING:=0}
+ - export RELEASE_TESTING=${TRAVIS_RELEASE_TESTING:=0}
+ - prove -l -j$(test-jobs) $(test-files)
after_success:
- - ./travis_scripts/trigger-dockerhub.sh
+ - coverage-report
+ - ./travis_scripts/trigger-dockerhub.sh
#TODO - send emails to bioperl-guts-l
notifications:
@@ -63,3 +83,4 @@ branches:
only:
- master
- /^release-[1-9]*-[0-9]*-[0-9]*$/
+ - network-cron-master
diff --git a/Bio/AlignIO/phylip.pm b/Bio/AlignIO/phylip.pm
index e6dcbaa..d694b00 100644
--- a/Bio/AlignIO/phylip.pm
+++ b/Bio/AlignIO/phylip.pm
@@ -10,37 +10,61 @@ Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
=head1 SYNOPSIS
-# Do not use this module directly. Use it via the Bio::AlignIO class.
+Do not use this module directly. Use it via the Bio::AlignIO class.
+
+This example shows how to write to phylip format:
use Bio::AlignIO;
use Bio::SimpleAlign;
- #you can set the name length to something other than the default 10
- #if you use a version of phylip (hacked) that accepts ids > 10
- my $phylipstream = Bio::AlignIO->new(-format => 'phylip',
- -fh => \*STDOUT,
- -idlength=>30);
- # convert data from one format to another
- my $gcgstream = Bio::AlignIO->new(-format => 'msf',
- -file => 't/data/cysprot1a.msf');
+
+ # Use -idlength to set the name length to something other than
+ # the default 10 if you need longer ids.
+ my $phylipstream = Bio::AlignIO->new(-format => 'phylip',
+ -fh => \*STDOUT,
+ -idlength => 30);
+ # Convert data from one format to another
+ my $gcgstream = Bio::AlignIO->new(-format => 'msf',
+ -file => 't/data/cysprot1a.msf');
while( my $aln = $gcgstream->next_aln ) {
$phylipstream->write_aln($aln);
}
- # do it again with phylip sequential format format
+ # With phylip sequential format format
$phylipstream->interleaved(0);
- # can also initialize the object like this
+ # Or initialize the object like this
$phylipstream = Bio::AlignIO->new(-interleaved => 0,
- -format => 'phylip',
- -fh => \*STDOUT,
- -idlength=>10);
- $gcgstream = Bio::AlignIO->new(-format => 'msf',
- -file => 't/data/cysprot1a.msf');
+ -format => 'phylip',
+ -fh => \*STDOUT,
+ -idlength => 20 );
+ $gcgstream = Bio::AlignIO->new(-format => 'msf',
+ -file => 't/data/cysprot1a.msf');
while( my $aln = $gcgstream->next_aln ) {
$phylipstream->write_aln($aln);
}
+This example shows how to read phylip format:
+
+ my $in = Bio::AlignIO->new(
+ -file => $inFile,
+ -format => 'phylip',
+ -interleaved => 0,
+ -longid => 1
+ );
+
+ my $out = Bio::AlignIO->new(
+ -file => ">$outFile",
+ -format => 'fasta'
+ );
+
+ while ( my $aln = $in->next_aln() ) {
+ $out->write_aln($aln);
+ }
+
+The -longid argument is required if the input phylip format file
+has ids with lengths greater then 10 characters.
+
=head1 DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from PHYLIP
@@ -48,9 +72,9 @@ format. By default it works with the interleaved format. By specifying
the flag -interleaved =E<gt> 0 in the initialization the module can
read or write data in sequential format.
-Long IDs up to 50 characters are supported by flag -longid =E<gt>
-1. ID strings can be surrounded by single quoted. They are mandatory
-only if the IDs contain spaces.
+Reading phylip format with long IDs up to 50 characters is supported by
+the flag -longid =E<gt>1. ID strings can be surrounded by single quotes.
+They are mandatory only if the IDs contain spaces.
=head1 FEEDBACK
@@ -92,30 +116,30 @@ use vars qw($DEFAULTIDLENGTH $DEFAULTLINELEN $DEFAULTTAGLEN);
use strict;
use Bio::SimpleAlign;
-use POSIX; # for the rounding call
+use POSIX; # for the rounding call
use base qw(Bio::AlignIO);
BEGIN {
$DEFAULTIDLENGTH = 10;
- $DEFAULTLINELEN = 60;
- $DEFAULTTAGLEN = 10;
+ $DEFAULTLINELEN = 60;
+ $DEFAULTTAGLEN = 10;
}
=head2 new
Title : new
Usage : my $alignio = Bio::AlignIO->new(-format => 'phylip'
- -file => '>file',
- -idlength => 10,
- -idlinebreak => 1);
+ -file => '>file',
+ -idlength => 10,
+ -idlinebreak => 1);
Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer
Returns : L<Bio::AlignIO> object
Args : [specific for writing of phylip format files]
-idlength => integer - length of the id (will pad w/
- spaces if needed)
+ spaces if needed) when writing phylip
-interleaved => boolean - whether interleaved
- or sequential format required
+ or sequential format required
-line_length => integer of how long a sequence lines should be
-idlinebreak => insert a line break after the sequence id
so that sequence starts on the next line
@@ -125,35 +149,39 @@ BEGIN {
each line between the space separator. set it
to 0 to have 1 tag only.
-wrap_sequential => boolean for whether or not sequential
- format should be broken up or a single line
- default is false (single line)
- -longid => boolean for allowing arbitrary long IDs (default is false)
+ format should be broken up or a single line
+ default is false (single line)
+ -longid => boolean to read arbitrary long IDs (default is false)
=cut
sub _initialize {
- my($self, at args) = @_;
- $self->SUPER::_initialize(@args);
-
- my ($interleave,$linelen,$idlinebreak,
- $idlength, $flag_SI, $tag_length,$ws, $longid) =
- $self->_rearrange([qw(INTERLEAVED
- LINE_LENGTH
- IDLINEBREAK
- IDLENGTH
- FLAG_SI
- TAG_LENGTH
- WRAP_SEQUENTIAL
- LONGID)], at args);
- $self->interleaved($interleave ? 1 : 0) if defined $interleave;
- $self->idlength($idlength || $DEFAULTIDLENGTH);
- $self->id_linebreak(1) if( $idlinebreak );
- $self->line_length($linelen) if defined $linelen && $linelen > 0;
- $self->flag_SI(1) if ( $flag_SI );
- $self->tag_length($tag_length) if ( $tag_length || $DEFAULTTAGLEN );
- $self->wrap_sequential($ws ? 1 : 0);
- $self->longid($longid ? 1 : 0);
- 1;
+ my ( $self, @args ) = @_;
+ $self->SUPER::_initialize(@args);
+
+ my ( $interleave, $linelen, $idlinebreak,
+ $idlength, $flag_SI, $tag_length, $ws, $longid )
+ = $self->_rearrange(
+ [ qw(INTERLEAVED
+ LINE_LENGTH
+ IDLINEBREAK
+ IDLENGTH
+ FLAG_SI
+ TAG_LENGTH
+ WRAP_SEQUENTIAL
+ LONGID)
+ ],
+ @args
+ );
+ $self->interleaved( $interleave ? 1 : 0 ) if defined $interleave;
+ $self->idlength( $idlength || $DEFAULTIDLENGTH );
+ $self->id_linebreak(1) if ($idlinebreak);
+ $self->line_length($linelen) if defined $linelen && $linelen > 0;
+ $self->flag_SI(1) if ($flag_SI);
+ $self->tag_length($tag_length) if ( $tag_length || $DEFAULTTAGLEN );
+ $self->wrap_sequential( $ws ? 1 : 0 );
+ $self->longid( $longid ? 1 : 0 );
+ 1;
}
=head2 next_aln
@@ -171,69 +199,77 @@ sub _initialize {
sub next_aln {
my $self = shift;
my $entry;
- my ($seqcount, $residuecount, %hash, $name,$str,
- @names,$seqname,$start,$end,$count,$seq);
+ my ($seqcount, $residuecount, %hash, $name,
+ $str, @names, $seqname, $start,
+ $end, $count, $seq
+ );
- my $aln = Bio::SimpleAlign->new(-source => 'phylip');
+ my $aln = Bio::SimpleAlign->new( -source => 'phylip' );
# First, parse up through the header.
# If we see a non-blank line that isn't the seqcount and residuecount line
# then bail out of next_aln (return)
- while ($entry = $self->_readline) {
- if ($entry =~ /^\s?$/) {
+ while ( $entry = $self->_readline ) {
+ if ( $entry =~ /^\s?$/ ) {
next;
- } elsif ($entry =~ /\s*(\d+)\s+(\d+)/) {
- ($seqcount, $residuecount) = ($1, $2);
+ } elsif ( $entry =~ /\s*(\d+)\s+(\d+)/ ) {
+ ( $seqcount, $residuecount ) = ( $1, $2 );
last;
} else {
- $self->warn ("Failed to parse PHYLIP: Did not see a sequence count and residue count.");
+ $self->warn(
+ "Failed to parse PHYLIP: Did not see a sequence count and residue count."
+ );
return;
}
}
return unless $seqcount and $residuecount;
-
- # First alignment section. We expect to see a name and (part of) a sequence.
+
+ # First alignment section. We expect to see a name and (part of) a sequence.
my $idlen = $self->idlength;
$count = 0;
- while ($entry = $self->_readline) {
- if ($entry =~ /^\s?$/) { # eat the newlines
+ while ( $entry = $self->_readline ) {
+ if ( $entry =~ /^\s?$/ ) { # eat the newlines
next;
}
- # Names can be in a few different formats:
- # 1. they can be traditional phylip: 10 chars long, period. If this is the case, that name can have spaces.
- # 2. they can be hacked with a long ID, as passed in with the flag -longid.
- # 3. if there is a long ID, the name can have spaces as long as it is wrapped in single quotes.
- if ($self->longid()) { # 2 or 3
- if ($entry =~ /^'(.+)'\s+(.+)$/) { # 3. name has single quotes.
+# Names can be in a few different formats:
+# 1. they can be traditional phylip: 10 chars long, period. If this is the case, that name can have spaces.
+# 2. they can be hacked with a long ID, as passed in with the flag -longid.
+# 3. if there is a long ID, the name can have spaces as long as it is wrapped in single quotes.
+ if ( $self->longid() ) { # 2 or 3
+ if ( $entry =~ /^'(.+)'\s+(.+)$/ ) { # 3. name has single quotes.
$name = $1;
- $str = $2;
- } else { # 2. name does not have single quotes, so should not have spaces.
- # therefore, the first part of the line is the name and the rest is the seq.
- # make sure that the line does not lead with extra spaces.
+ $str = $2;
+ } else { # 2. name does not have single quotes, so should not have spaces.
+ # therefore, the first part of the line is the name and the rest is the seq.
+ # make sure that the line does not lead with extra spaces.
$entry =~ s/^\s+//;
- ($name, $str) = split (/\s+/,$entry, 2);
+ ( $name, $str ) = split( /\s+/, $entry, 2 );
}
- } else { # 1. traditional phylip.
+ } else { # 1. traditional phylip.
$entry =~ /^(.{1,10})\s(.+)$/;
$name = $1;
- $str = $2;
- $name =~ s/\s+$//; # eat any trailing spaces
+ $str = $2;
+ $name =~ s/\s+$//; # eat any trailing spaces
$name =~ s/\s+/_/g;
}
push @names, $name;
+
#clean sequence of spaces:
$str =~ s/\s+//g;
- # are we sequential? If so, we should keep adding to the sequence until we've got all the residues.
- if (($self->interleaved) == 0) {
- while (length($str) < $residuecount) {
+# are we sequential? If so, we should keep adding to the sequence until we've got all the residues.
+ if ( ( $self->interleaved ) == 0 ) {
+ while ( length($str) < $residuecount ) {
$entry = $self->_readline;
$str .= $entry;
$str =~ s/\s+//g;
- if ($entry =~ /^\s*$/) { # we ran into a newline before we got a complete sequence: bail!
- $self->warn("Failed to parse PHYLIP: Sequence $name was shorter than expected: " . length($str) . " instead of $residuecount.");
+ if ( $entry =~ /^\s*$/ ) { # we ran into a newline before we got a complete sequence: bail!
+ $self->warn(
+ "Failed to parse PHYLIP: Sequence $name was shorter than expected: "
+ . length($str)
+ . " instead of $residuecount." );
last;
}
}
@@ -241,46 +277,57 @@ sub next_aln {
$hash{$count} = $str;
$count++;
+
# if we've read as many seqs as we're supposed to, move on.
- if ($count == $seqcount) {
+ if ( $count == $seqcount ) {
last;
}
}
- # if we are interleaved, we're going to keep seeing chunks of sequence until we get all of it.
- if ($self->interleaved) {
- while (length($hash{$seqcount-1}) < $residuecount) {
+# if we are interleaved, we're going to keep seeing chunks of sequence until we get all of it.
+ if ( $self->interleaved ) {
+ while ( length( $hash{ $seqcount - 1 } ) < $residuecount ) {
$count = 0;
- while ($entry = $self->_readline) {
- if ($entry =~ /^\s*$/) { # eat newlines
- if ($count != 0) { # there was a newline at an unexpected place!
- $self->warn("Failed to parse PHYLIP: Interleaved file is missing a segment: saw $count, expected $seqcount.");
+ while ( $entry = $self->_readline ) {
+ if ( $entry =~ /^\s*$/ ) { # eat newlines
+ if ( $count != 0 ) { # there was a newline at an unexpected place!
+ $self->warn(
+ "Failed to parse PHYLIP: Interleaved file is missing a segment: saw $count, expected $seqcount."
+ );
return;
}
next;
- } else { # start taking in chunks
+ } else { # start taking in chunks
$entry =~ s/\s//g;
$hash{$count} .= $entry;
$count++;
}
- if ($count >= $seqcount) { # we've read all of the sequences for this chunk, so move on.
+ if ( $count >= $seqcount ) { # we've read all of the sequences for this chunk, so move on.
last;
}
}
}
}
- if ((scalar @names) != $seqcount) {
- $self->warn("Failed to parse PHYLIP: Did not see the correct number of seqs: saw " . scalar(@names) . ", expected $seqcount.");
+ if ( ( scalar @names ) != $seqcount ) {
+ $self->warn(
+ "Failed to parse PHYLIP: Did not see the correct number of seqs: saw "
+ . scalar(@names)
+ . ", expected $seqcount." );
return;
}
- for ($count=0; $count<$seqcount; $count++) {
+ for ( $count = 0; $count < $seqcount; $count++ ) {
$str = $hash{$count};
my $seqname = $names[$count];
- if (length($str) != $residuecount) {
- $self->warn("Failed to parse PHYLIP: Sequence $seqname was the wrong length: " . length($str) . " instead of $residuecount.");
+ if ( length($str) != $residuecount ) {
+ $self->warn(
+ "Failed to parse PHYLIP: Sequence $seqname was the wrong length: "
+ . length($str)
+ . " instead of $residuecount." );
}
- $seq = Bio::LocatableSeq->new('-seq' => $hash{$count},
- '-display_id' => $seqname);
+ $seq = Bio::LocatableSeq->new(
+ '-seq' => $hash{$count},
+ '-display_id' => $seqname
+ );
$aln->add_seq($seq);
}
return $aln;
@@ -297,109 +344,136 @@ sub next_aln {
=cut
sub write_aln {
- my ($self, at aln) = @_;
- my $count = 0;
+ my ( $self, @aln ) = @_;
+ my $count = 0;
my $wrapped = 0;
my $maxname;
my $width = $self->line_length();
- my ($length,$date,$name,$seq,$miss,$pad,
- %hash, at arr,$tempcount,$index,$idlength,$flag_SI,$line_length, $tag_length);
+ my ($length, $date, $name, $seq, $miss,
+ $pad, %hash, @arr, $tempcount, $index,
+ $idlength, $flag_SI, $line_length, $tag_length
+ );
foreach my $aln (@aln) {
- if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
- $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
- next;
- }
- $self->throw("All sequences in the alignment must be the same length")
- unless $aln->is_flush(1) ;
+ if ( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
+ $self->warn(
+ "Must provide a Bio::Align::AlignI object when calling write_aln"
+ );
+ next;
+ }
+ $self->throw("All sequences in the alignment must be the same length")
+ unless $aln->is_flush(1);
$flag_SI = $self->flag_SI();
- $aln->set_displayname_flat(); # plain
- $length = $aln->length();
+ $aln->set_displayname_flat(); # plain
+ $length = $aln->length();
if ($flag_SI) {
- if ($self->interleaved() ) {
- $self->_print (sprintf(" %s %s I\n", $aln->num_sequences, $aln->length));
+ if ( $self->interleaved() ) {
+ $self->_print(
+ sprintf(
+ " %s %s I\n", $aln->num_sequences, $aln->length
+ )
+ );
} else {
- $self->_print (sprintf(" %s %s S\n", $aln->num_sequences, $aln->length));
+ $self->_print(
+ sprintf(
+ " %s %s S\n", $aln->num_sequences, $aln->length
+ )
+ );
}
} else {
- $self->_print (sprintf(" %s %s\n", $aln->num_sequences, $aln->length));
+ $self->_print(
+ sprintf( " %s %s\n", $aln->num_sequences, $aln->length ) );
+ }
+
+ $idlength = $self->idlength();
+ $line_length = $self->line_length();
+ $tag_length = $self->tag_length();
+ foreach $seq ( $aln->each_seq() ) {
+ $name = $aln->displayname( $seq->get_nse );
+ if ( $self->longid ) {
+ $self->warn(
+ "The length of the name is over 50 chars long [$name]")
+ if length($name) > 50;
+ $name = "'$name' ";
+ } else {
+ $name = substr( $name, 0, $idlength )
+ if length($name) > $idlength;
+ $name = sprintf( "%-" . $idlength . "s", $name );
+ if ( $self->interleaved() ) {
+ $name .= ' ';
+ } elsif ( $self->id_linebreak ) {
+ $name .= "\n";
+ }
+ }
+
+ #phylip needs dashes not dots
+ my $seq = $seq->seq();
+ $seq =~ s/\./-/g;
+ $hash{$name} = $seq;
+ push( @arr, $name );
}
- $idlength = $self->idlength();
- $line_length = $self->line_length();
- $tag_length = $self->tag_length();
- foreach $seq ( $aln->each_seq() ) {
- $name = $aln->displayname($seq->get_nse);
- if ($self->longid) {
- $self->warn("The length of the name is over 50 chars long [$name]")
- if length($name) > 50;
- $name = "'$name' "
- } else {
- $name = substr($name, 0, $idlength) if length($name) > $idlength;
- $name = sprintf("%-".$idlength."s",$name);
- if( $self->interleaved() ) {
- $name .= ' ' ;
- } elsif( $self->id_linebreak) {
- $name .= "\n";
- }
- }
- #phylip needs dashes not dots
- my $seq = $seq->seq();
- $seq =~ s/\./-/g;
- $hash{$name} = $seq;
- push(@arr,$name);
- }
-
- if( $self->interleaved() ) {
+ if ( $self->interleaved() ) {
my $numtags;
- if ($tag_length <= $line_length) {
- $numtags = floor($line_length/$tag_length);
- $line_length = $tag_length*$numtags;
+ if ( $tag_length <= $line_length ) {
+ $numtags = floor( $line_length / $tag_length );
+ $line_length = $tag_length * $numtags;
} else {
$numtags = 1;
}
- while( $count < $length ) {
-
- # there is another block to go!
- foreach $name ( @arr ) {
- my $dispname = $name;
- $dispname = '' if $wrapped;
- $self->_print (sprintf("%".($idlength+3)."s",$dispname));
- $tempcount = $count;
- $index = 0;
- $self->debug("residue count: $count\n") if ($count%100000 == 0);
- while( ($tempcount + $tag_length < $length) &&
- ($index < $numtags) ) {
- $self->_print (sprintf("%s ",substr($hash{$name},
- $tempcount,
- $tag_length)));
- $tempcount += $tag_length;
- $index++;
- }
- # last
- if( $index < $numtags) {
- # space to print!
- $self->_print (sprintf("%s",substr($hash{$name},
- $tempcount)));
- $tempcount += $tag_length;
- }
- $self->_print ("\n");
- }
- $self->_print ("\n");
- $count = $tempcount;
- $wrapped = 1;
- }
- } else {
- foreach $name ( @arr ) {
- my $dispname = $name;
- my $line = sprintf("%s%s\n",$dispname,$hash{$name});
- if( $self->wrap_sequential ) {
- $line =~ s/(.{1,$width})/$1\n/g;
- }
- $self->_print ($line);
- }
- }
+ while ( $count < $length ) {
+
+ # there is another block to go!
+ foreach $name (@arr) {
+ my $dispname = $name;
+ $dispname = '' if $wrapped;
+ $self->_print(
+ sprintf( "%" . ( $idlength + 3 ) . "s", $dispname ) );
+ $tempcount = $count;
+ $index = 0;
+ $self->debug("residue count: $count\n")
+ if ( $count % 100000 == 0 );
+ while (( $tempcount + $tag_length < $length )
+ && ( $index < $numtags ) ) {
+ $self->_print(
+ sprintf(
+ "%s ",
+ substr(
+ $hash{$name}, $tempcount, $tag_length
+ )
+ )
+ );
+ $tempcount += $tag_length;
+ $index++;
+ }
+
+ # last
+ if ( $index < $numtags ) {
+
+ # space to print!
+ $self->_print(
+ sprintf( "%s",
+ substr( $hash{$name}, $tempcount ) )
+ );
+ $tempcount += $tag_length;
+ }
+ $self->_print("\n");
+ }
+ $self->_print("\n");
+ $count = $tempcount;
+ $wrapped = 1;
+ }
+ } else {
+ foreach $name (@arr) {
+ my $dispname = $name;
+ my $line = sprintf( "%s%s\n", $dispname, $hash{$name} );
+ if ( $self->wrap_sequential ) {
+ $line =~ s/(.{1,$width})/$1\n/g;
+ }
+ $self->_print($line);
+ }
+ }
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
@@ -417,13 +491,16 @@ sub write_aln {
=cut
sub interleaved {
- my ($self,$value) = @_;
- if( defined $value ) {
- if ($value) {$self->{'_interleaved'} = 1 }
- else {$self->{'_interleaved'} = 0 }
- }
- return 1 unless defined $self->{'_interleaved'};
- return $self->{'_interleaved'};
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ if ($value) {
+ $self->{'_interleaved'} = 1
+ } else {
+ $self->{'_interleaved'} = 0
+ }
+ }
+ return 1 unless defined $self->{'_interleaved'};
+ return $self->{'_interleaved'};
}
=head2 flag_SI
@@ -439,13 +516,13 @@ sub interleaved {
=cut
-sub flag_SI{
- my ($self,$value) = @_;
- my $previous = $self->{'_flag_SI'};
- if( defined $value ) {
- $self->{'_flag_SI'} = $value;
- }
- return $previous;
+sub flag_SI {
+ my ( $self, $value ) = @_;
+ my $previous = $self->{'_flag_SI'};
+ if ( defined $value ) {
+ $self->{'_flag_SI'} = $value;
+ }
+ return $previous;
}
=head2 idlength
@@ -460,11 +537,11 @@ sub flag_SI{
=cut
sub idlength {
- my($self,$value) = @_;
- if (defined $value){
- $self->{'_idlength'} = $value;
- }
- return $self->{'_idlength'};
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_idlength'} = $value;
+ }
+ return $self->{'_idlength'};
}
=head2 line_length
@@ -478,10 +555,10 @@ sub idlength {
=cut
-sub line_length{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_line_length'} = $value;
+sub line_length {
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_line_length'} = $value;
}
return $self->{'_line_length'} || $DEFAULTLINELEN;
@@ -499,15 +576,14 @@ sub line_length{
=cut
-sub tag_length{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_tag_length'} = $value;
+sub tag_length {
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_tag_length'} = $value;
}
return $self->{'_tag_length'} || $DEFAULTTAGLEN;
}
-
=head2 id_linebreak
Title : id_linebreak
@@ -519,15 +595,14 @@ sub tag_length{
=cut
-sub id_linebreak{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_id_linebreak'} = $value;
+sub id_linebreak {
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_id_linebreak'} = $value;
}
return $self->{'_id_linebreak'} || 0;
}
-
=head2 wrap_sequential
Title : wrap_sequential
@@ -539,10 +614,10 @@ sub id_linebreak{
=cut
-sub wrap_sequential{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_wrap_sequential'} = $value;
+sub wrap_sequential {
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_wrap_sequential'} = $value;
}
return $self->{'_wrap_sequential'} || 0;
}
@@ -558,10 +633,10 @@ sub wrap_sequential{
=cut
-sub longid{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_longid'} = $value;
+sub longid {
+ my ( $self, $value ) = @_;
+ if ( defined $value ) {
+ $self->{'_longid'} = $value;
}
return $self->{'_longid'} || 0;
}
diff --git a/Bio/AlignIO/xmfa.pm b/Bio/AlignIO/xmfa.pm
index 089d227..fd4b81d 100644
--- a/Bio/AlignIO/xmfa.pm
+++ b/Bio/AlignIO/xmfa.pm
@@ -12,7 +12,7 @@ Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
=head1 SYNOPSIS
-Do not use this module directly. Use it via the L<Bio::AlignIO>
+Do not use this module directly. Use it via the L<Bio::AlignIO>
class.
=head1 DESCRIPTION
@@ -27,20 +27,20 @@ Peter Schattner
=head1 TODO
-Finish write_aln(), clean up code, allow LargeLocatableSeq (ie for
-very large sequences a'la Mauve)
+Finish write_aln(), clean up code, allow LargeLocatableSeq (e.g. for
+very large sequences from Mauve).
=head1 FEEDBACK
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -117,7 +117,7 @@ sub next_aln {
$seqchar .= $entry;
}
}
-
+
# this catches last sequence if '=' is not present (Mauve)
if ( defined $name ) {
my $seq = $self->_process_seq($name, $seqchar);
@@ -144,7 +144,7 @@ sub write_aln {
my ($seq,$desc,$rseq,$name,$count,$length,$seqsub,$start,$end,$strand,$id);
foreach my $aln (@aln) {
- if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
+ if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
@@ -161,7 +161,7 @@ sub write_aln {
$name = sprintf("%d:%d-%d %s %s",$seqct,$start,$end,$strand,$id);
$seq = $rseq->seq();
$desc = $rseq->description || '';
- $self->_print (">$name $desc\n") or return ;
+ $self->_print (">$name $desc\n") or return ;
$count = 0;
$length = length($seq);
if(defined $seq && $length > 0) {
@@ -175,7 +175,7 @@ sub write_aln {
my $alndesc = '';
$alndesc = "score = ".$aln->score if ($aln->score);
$self->_print("= $alndesc\n") || return 0;
-
+
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
@@ -184,7 +184,7 @@ sub write_aln {
=head2 _get_len
Title : _get_len
- Usage :
+ Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
@@ -203,7 +203,7 @@ sub _get_len {
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
- Returns : integer value of width
+ Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
@@ -222,9 +222,11 @@ sub _process_seq {
my ($self, $entry, $seq) = @_;
my ($start, $end, $strand, $seqname, $desc, $all);
# put away last name and sequence
- if ( $entry =~ m{^>\s*\d+:(\d+)-(\d+)\s([+-]{1})(?:\s+(\S+)\s*(\S\.*)?)?} ) {
+ if ( $entry =~ m{^>\s*\d+:(\d+)-(\d+)\s+([+-]{1})(?:\s+(\S+)\s*(\S\.*)?)?} ) {
($start, $end, $seqname, $desc) = ($1, $2, $4, $5);
$strand = ($3 eq '+') ? 1 : -1;
+ } elsif ( $entry !~ /^>\s*\d+:/ ) {
+ $self->throw("First field after '>' must be a number:\n$entry");
} else {
$self->throw("Line does not comform to XMFA format:\n$entry");
}
diff --git a/Bio/AnalysisI.pm b/Bio/AnalysisI.pm
index c0fb99d..4b97957 100644
--- a/Bio/AnalysisI.pm
+++ b/Bio/AnalysisI.pm
@@ -676,7 +676,7 @@ keys:
ended
elapsed
-See C<create> for remarks on time formating.
+See C<create> for remarks on time formatting.
An example - both for unformatted and formatted times:
diff --git a/Bio/Annotation/OntologyTerm.pm b/Bio/Annotation/OntologyTerm.pm
index a9c339a..7525732 100644
--- a/Bio/Annotation/OntologyTerm.pm
+++ b/Bio/Annotation/OntologyTerm.pm
@@ -341,7 +341,7 @@ sub definition {
another Term (e.g. the top level of the ontology).
Returns : The ontology of this Term [TermI].
Args : The ontology of this Term [TermI or scalar -- which
- becomes the name of the catagory term] (optional).
+ becomes the name of the category term] (optional).
=cut
diff --git a/Bio/AnnotationCollectionI.pm b/Bio/AnnotationCollectionI.pm
index 33acdfb..f1bc2e8 100644
--- a/Bio/AnnotationCollectionI.pm
+++ b/Bio/AnnotationCollectionI.pm
@@ -47,7 +47,7 @@ The Bioperl approach is that the "interesting facts" are represented by
Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees
two methods
- $obj->as_text(); # string formated to display to users
+ $obj->as_text(); # string formatted to display to users
and
diff --git a/Bio/Assembly/Contig.pm b/Bio/Assembly/Contig.pm
index 60be852..ad9fa58 100644
--- a/Bio/Assembly/Contig.pm
+++ b/Bio/Assembly/Contig.pm
@@ -2,7 +2,7 @@
# BioPerl module for Bio::Assembly::Contig
# Mostly based on Bio::SimpleAlign by Ewan Birney
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Robson Francisco de Souza <rfsouza at citri.iq.usp.br>
#
@@ -103,7 +103,7 @@ of the aligned sequences that were used to do the assembly.
"gapped consensus" refers to positions in the aligned consensus
sequence, which is the consensus sequence including the gaps inserted
-to align it agains the aligned sequences that were used to assemble
+to align it against the aligned sequences that were used to assemble
the contig. So, its limits are [ 1, (consensus length + number of gaps
in consensus) ]
@@ -184,15 +184,15 @@ Bioperl mailing lists Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -266,8 +266,8 @@ sub new {
$self->{'_nof_residues'} = 0;
$self->{'_nof_seqs'} = 0;
# $self->{'_nof_segments'} = 0; # Let's not make it heavier than needed by now...
-
- # for cases where SF::Collection is shared between Bio::Assembly::Contig
+
+ # for cases where SF::Collection is shared between Bio::Assembly::Contig
if ($collection) {
$self->throw("Collection must implement Bio::SeqFeature::CollectionI") unless $collection->isa('Bio::SeqFeature::CollectionI');
$self->{'_sfc'} = $collection;
@@ -331,7 +331,7 @@ sub assembly {
if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold"));
# We create a circular reference to a Scaffold object. It is made weak
# to prevent memory leaks.
- $self->{'_assembly'} = $assembly if (defined $assembly);
+ $self->{'_assembly'} = $assembly if (defined $assembly);
weaken($self->{'_assembly'});
return $self->{'_assembly'};
@@ -424,7 +424,7 @@ sub downstream_neighbor {
the feature attached to one of the contig aligned
sequences, the feature is registered as an aligned
sequence feature. If $flag is 0 and the feature is not
- attched to any sequence in the contig, the feature is
+ attached to any sequence in the contig, the feature is
simply added to the feature collection and no attachment
or registration is made.
@@ -495,7 +495,7 @@ sub remove_features {
$self->{'_elem'}{$seqID}{'_feat'}{$tag} eq $feat);
}
}
-
+
# Removing Bio::SeqFeature objects
return $self->get_features_collection->delete(@args);
}
@@ -1137,11 +1137,11 @@ sub add_seq {
# Our locatable sequences are always considered to be complete sequences
$seq->start(1);
$seq->end($seq->_ungapped_len);
-
+
my $alphabet = $seq->alphabet;
-
+
$alphabet = lc($alphabet) if defined $alphabet;
-
+
$self->warn("Adding non-nucleotidic sequence ".$seqID)
if (!$alphabet || ($alphabet ne 'dna' && $alphabet ne 'rna'));
@@ -1205,10 +1205,10 @@ sub remove_seq {
# Updating residue count
$self->{'_nof_residues'} -= $seq->length() +
&_nof_gaps( $self->{'_elem'}{$seqID}{'_gaps'}, $seq->length );
-
+
# Update number of sequences
- $self->{'_nof_seqs'}--;
-
+ $self->{'_nof_seqs'}--;
+
# Update order of sequences (order starts at 1)
my $max_order = $self->{'_nof_seqs'} + 1;
my $target_order = $max_order + 1;
@@ -1267,7 +1267,7 @@ sub purge {
Usage : $contig->sort_alphabetically
Function :
- Changes the order of the alignemnt to alphabetical on name
+ Changes the order of the alignment to alphabetical on name
followed by numerical by number.
Returns :
@@ -1461,7 +1461,7 @@ alignment.
Notice that the from (arg1) is interpretted as a regex,
so be careful about quoting meta characters (eg
- $contig->map_chars('.','-') wont do what you want)
+ $contig->map_chars('.','-') won't do what you want)
Returns :
Argument : 'from' rexexp
@@ -2169,7 +2169,7 @@ sub _register_gaps {
Function : number of residues in total in the alignment
Returns : integer
Argument :
- Note : deprecated in favor of num_residues()
+ Note : deprecated in favor of num_residues()
=cut
diff --git a/Bio/Assembly/ScaffoldI.pm b/Bio/Assembly/ScaffoldI.pm
index dbfb485..864c398 100644
--- a/Bio/Assembly/ScaffoldI.pm
+++ b/Bio/Assembly/ScaffoldI.pm
@@ -9,7 +9,7 @@
=head1 NAME
-Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
+Bio::Assembly::ScaffoldI - Abstract Interface of Sequence Assemblies
=head1 SYNOPSIS
diff --git a/Bio/Assembly/Singlet.pm b/Bio/Assembly/Singlet.pm
index 0122529..f369f41 100644
--- a/Bio/Assembly/Singlet.pm
+++ b/Bio/Assembly/Singlet.pm
@@ -136,7 +136,7 @@ sub seqref {
Title : _seq_to_singlet
Usage : $singlet->seqref($seq)
Function: Transform a sequence into a singlet
- Returns : 1 for sucess
+ Returns : 1 for success
Args : A Bio::Seq-compliant object
=cut
diff --git a/Bio/Assembly/Tools/ContigSpectrum.pm b/Bio/Assembly/Tools/ContigSpectrum.pm
index 05cdb60..7467848 100644
--- a/Bio/Assembly/Tools/ContigSpectrum.pm
+++ b/Bio/Assembly/Tools/ContigSpectrum.pm
@@ -1819,7 +1819,7 @@ sub _update_overlap_stats {
Args : Bio::Assembly::Contig object reference
Bio::LocatableSeq contig sequence 1
Bio::LocatableSeq contig sequence 2
- minium overlap length [optional]
+ minimum overlap length [optional]
minimum overlap identity percentage[optional]
=cut
diff --git a/Bio/Cluster/UniGene.pm b/Bio/Cluster/UniGene.pm
index 1fedd35..d4c64e8 100644
--- a/Bio/Cluster/UniGene.pm
+++ b/Bio/Cluster/UniGene.pm
@@ -836,7 +836,7 @@ sub annotation{
Usage :
Function: Adds a member object to the list of members.
Example :
- Returns : TRUE if the new member was successfuly added, and FALSE
+ Returns : TRUE if the new member was successfully added, and FALSE
otherwise.
Args : The member to add.
@@ -1169,7 +1169,7 @@ sub namespace {
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
- user of this interface would not assumme this) and should be
+ user of this interface would not assume this) and should be
less than thirty characters (though again, double checking
this is a good idea)
diff --git a/Bio/DB/EMBL.pm b/Bio/DB/EMBL.pm
index 3b1fb3f..5d5eef5 100644
--- a/Bio/DB/EMBL.pm
+++ b/Bio/DB/EMBL.pm
@@ -41,7 +41,7 @@ Bio::DB::EMBL - Database object interface for EMBL entry retrieval
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
- # also don't want features, just sequence so let's save bandwith
+ # also don't want features, just sequence so let's save bandwidth
# and request Fasta sequence
$embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
-format => 'fasta');
diff --git a/Bio/DB/Fasta.pm b/Bio/DB/Fasta.pm
index 79d0413..e150d20 100644
--- a/Bio/DB/Fasta.pm
+++ b/Bio/DB/Fasta.pm
@@ -70,7 +70,7 @@ specific portion of the gi|gb|abc|xyz GenBank IDs.
=head1 DATABASE CREATION AND INDEXING
The object-oriented constructor is new(), the filehandle constructor is newFh()
-and the tied hash constructor is tie(). They all allow to index a single Fasta
+and the tied hash constructor is tie(). They all allow one to index a single Fasta
file, several files, or a directory of files. See Bio::DB::IndexedBase.
=head1 SEE ALSO
diff --git a/Bio/DB/Flat/BinarySearch.pm b/Bio/DB/Flat/BinarySearch.pm
index 041b5ac..47fe5eb 100644
--- a/Bio/DB/Flat/BinarySearch.pm
+++ b/Bio/DB/Flat/BinarySearch.pm
@@ -363,7 +363,7 @@ sub get_Seq_by_id {
);
}
else {
- $self->{_seqio}->fh($fh);
+ $self->{_seqio}->_fh($fh);
}
return $self->{_seqio}->next_seq;
diff --git a/Bio/DB/GFF.pm b/Bio/DB/GFF.pm
index eb3751e..6f35a1d 100644
--- a/Bio/DB/GFF.pm
+++ b/Bio/DB/GFF.pm
@@ -696,7 +696,7 @@ adaptor-specific arguments:
-refclass landmark Class; defaults to "Sequence"
-The commonly used 'dbi::mysqlopt' adaptor also recogizes the following
+The commonly used 'dbi::mysqlopt' adaptor also recognizes the following
arguments.
Argument Description
@@ -2978,7 +2978,7 @@ sub get_features{
Status : abstract
This method is used internally. The callback arguments are the same
-as those used by make_feature(). This method must be overidden by
+as those used by make_feature(). This method must be overridden by
subclasses.
=cut
@@ -3008,7 +3008,7 @@ This method is used internally to fetch features either by their ID or
their group ID. $ids is a arrayref containing a list of IDs, $type is
one of "feature" or "group", and $callback is a callback. The
callback arguments are the same as those used by make_feature(). This
-method must be overidden by subclasses.
+method must be overridden by subclasses.
=cut
diff --git a/Bio/DB/GFF/Adaptor/dbi.pm b/Bio/DB/GFF/Adaptor/dbi.pm
index f31e9aa..25ac3b1 100644
--- a/Bio/DB/GFF/Adaptor/dbi.pm
+++ b/Bio/DB/GFF/Adaptor/dbi.pm
@@ -2165,7 +2165,7 @@ you want to calculate the coverage density. An object is returned
corresponding to the requested region. It contains a tag called
"coverage" that will return an array ref of "bins" length. Each
element of the array describes the number of features that overlap the
-bin at this postion.
+bin at this position.
Arguments:
diff --git a/Bio/DB/GFF/Adaptor/dbi/mysql.pm b/Bio/DB/GFF/Adaptor/dbi/mysql.pm
index 0c22ee1..cb43cee 100644
--- a/Bio/DB/GFF/Adaptor/dbi/mysql.pm
+++ b/Bio/DB/GFF/Adaptor/dbi/mysql.pm
@@ -111,7 +111,7 @@ This is the feature data table. Its columns are:
fid feature ID (integer)
fref reference sequence name (string)
fstart start position relative to reference (integer)
- fstop stop postion relative to reference (integer)
+ fstop stop position relative to reference (integer)
ftypeid feature type ID (integer)
fscore feature score (float); may be null
fstrand strand; one of "+" or "-"; may be null
diff --git a/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm b/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
index 96ed187..a977b6d 100644
--- a/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
+++ b/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
@@ -112,7 +112,7 @@ This is the feature data table. Its columns are:
fid feature ID (integer)
fref reference sequence name (string)
fstart start position relative to reference (integer)
- fstop stop postion relative to reference (integer)
+ fstop stop position relative to reference (integer)
ftypeid feature type ID (integer)
fscore feature score (float); may be null
fstrand strand; one of "+" or "-"; may be null
diff --git a/Bio/DB/GFF/Adaptor/dbi/oracle.pm b/Bio/DB/GFF/Adaptor/dbi/oracle.pm
index d9a8c47..0423e4d 100644
--- a/Bio/DB/GFF/Adaptor/dbi/oracle.pm
+++ b/Bio/DB/GFF/Adaptor/dbi/oracle.pm
@@ -120,7 +120,7 @@ This is the feature data table. Its columns are:
fid feature ID (integer)
fref reference sequence name (string)
fstart start position relative to reference (integer)
- fstop stop postion relative to reference (integer)
+ fstop stop position relative to reference (integer)
ftypeid feature type ID (integer)
fscore feature score (float); may be null
fstrand strand; one of "+" or "-"; may be null
diff --git a/Bio/DB/GFF/Adaptor/dbi/pg.pm b/Bio/DB/GFF/Adaptor/dbi/pg.pm
index 4dbc727..d178440 100644
--- a/Bio/DB/GFF/Adaptor/dbi/pg.pm
+++ b/Bio/DB/GFF/Adaptor/dbi/pg.pm
@@ -176,7 +176,7 @@ This is the feature data table. Its columns are:
fid feature ID (integer)
fref reference sequence name (string)
fstart start position relative to reference (integer)
- fstop stop postion relative to reference (integer)
+ fstop stop position relative to reference (integer)
ftypeid feature type ID (integer)
fscore feature score (float); may be null
fstrand strand; one of "+" or "-"; may be null
diff --git a/Bio/DB/GFF/Segment.pm b/Bio/DB/GFF/Segment.pm
index 364591b..9521097 100644
--- a/Bio/DB/GFF/Segment.pm
+++ b/Bio/DB/GFF/Segment.pm
@@ -593,7 +593,7 @@ sub seq_id { shift->refseq }
Status : Public
This indicates that the sequence was truncated during creation. The
-returned flag is undef if no truncation occured. If truncation did
+returned flag is undef if no truncation occurred. If truncation did
occur, the flag is actually an array ref in which the first element is
true if truncation occurred on the left, and the second element
occurred if truncation occurred on the right.
@@ -677,7 +677,7 @@ sub overlap_extent {
Usage : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
implementation. This allows implementations to manage their
- own object ids in a way the implementaiton can control
+ own object ids in a way the implementation can control
clients can expect one id to map to one object.
For sequences with no accession number, this method should
@@ -742,7 +742,7 @@ sub display_name { shift->seq_id }
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
- unique id for the implemetation, allowing multiple objects
+ unique id for the implementation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
diff --git a/Bio/DB/GenBank.pm b/Bio/DB/GenBank.pm
index a19a8fd..653b529 100644
--- a/Bio/DB/GenBank.pm
+++ b/Bio/DB/GenBank.pm
@@ -54,7 +54,7 @@ Bio::DB::GenBank - Database object interface to GenBank
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
- # also don't want features, just sequence so let's save bandwith
+ # also don't want features, just sequence so let's save bandwidth
# and request Fasta sequence
$gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' ,
-format => 'Fasta');
diff --git a/Bio/DB/GenPept.pm b/Bio/DB/GenPept.pm
index 9f3e1bc..dbb70e9 100644
--- a/Bio/DB/GenPept.pm
+++ b/Bio/DB/GenPept.pm
@@ -184,7 +184,7 @@ sub default_format {
Usage : $seq = $db->get_Seq_by_acc('AAC73346');
Function: Gets a Seq objects by accession number
Returns : Bio::Seq object
- Args : accession number to retrive by
+ Args : accession number to retrieve by
=head1 Routines implemented by Bio::DB::NCBIHelper
diff --git a/Bio/DB/GenericWebAgent.pm b/Bio/DB/GenericWebAgent.pm
index d20923a..8681451 100644
--- a/Bio/DB/GenericWebAgent.pm
+++ b/Bio/DB/GenericWebAgent.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::GenericWebAgent
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
@@ -21,7 +21,7 @@ access and response retrieval.
=head1 SYNOPSIS
# DO NOT USE DIRECTLY
-
+
See Bio::DB::EUtilities for an example implementation
=head1 DESCRIPTION
@@ -34,7 +34,7 @@ the user agent (Bio::ParameterBaseI), and a BioPerl class parser that processes
response content received by the user agent. The Bio::ParameterBaseI object
should be state-aware, e.g. know when changes occur to parameters, so that
identical requests are not repeatedly sent to the server (this base class takes
-this into consideration).
+this into consideration).
=head1 FEEDBACK
@@ -47,17 +47,17 @@ of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l at lists.open-bio.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -106,7 +106,7 @@ BEGIN {
Title : new
Usage : Bio::DB::GenericWebAgent->new(@args);
Function: Create new Bio::DB::GenericWebAgent instance.
- Returns :
+ Returns :
Args : None specific to this base class. Inheriting classes will
likely set specific parameters in their constructor;
Bio::DB::GenericWebAgent is primarily a test bed.
@@ -173,7 +173,7 @@ sub ua {
Returns : HTTP::Response object or data if callback is used
Args : (optional)
- -cache_response - flag to cache HTTP::Response object;
+ -cache_response - flag to cache HTTP::Response object;
Default is 1 (TRUE, caching ON)
These are passed on to LWP::UserAgent::request() if stipulated
@@ -193,7 +193,7 @@ sub get_Response {
my ($cache, $file, $cb, $size) = $self->_rearrange([qw(CACHE_RESPONSE FILE CB READ_SIZE_HINT)], at args);
$self->throw("Can't have both callback and file") if $file && $cb;
# make -file accept more perl-like write-append type data.
- $file =~ s{^>}{} if $file;
+ $file =~ s{^>}{} if $file;
my @opts = grep {defined $_} ($file || $cb, $size);
$cache = (defined $cache && $cache == 0) ? 0 : 1;
my $pobj = $self->parameter_base;
@@ -224,7 +224,7 @@ sub get_Response {
$cb && ref($cb) eq 'CODE' && $cb->($self->{_response_cache}->content);
}
return $self->{_response_cache};
- }
+ }
}
=head2 get_Parser
diff --git a/Bio/DB/HIV/HIVQueryHelper.pm b/Bio/DB/HIV/HIVQueryHelper.pm
index 49c270a..8e258fb 100755
--- a/Bio/DB/HIV/HIVQueryHelper.pm
+++ b/Bio/DB/HIV/HIVQueryHelper.pm
@@ -2046,7 +2046,7 @@ use Bio::Annotation::SimpleValue;
Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
- Function: access the annotation value assocated with the given tags
+ Function: access the annotation value associated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree
diff --git a/Bio/DB/IndexedBase.pm b/Bio/DB/IndexedBase.pm
index f054003..88aea4a 100644
--- a/Bio/DB/IndexedBase.pm
+++ b/Bio/DB/IndexedBase.pm
@@ -4,7 +4,6 @@
# You may distribute this module under the same terms as perl itself
#
-
=head1 NAME
Bio::DB::IndexedBase - Base class for modules using indexed sequence files
@@ -127,7 +126,7 @@ use tied(%db) to recover the Bio::DB::IndexedBase object and call its methods.
}
In addition, you may invoke the FIRSTKEY and NEXTKEY tied hash methods directly
-to retrieve the first and next ID in the database, respectively. This allows to
+to retrieve the first and next ID in the database, respectively. This allows one to
write the following iterative loop using just the object-oriented interface:
my $db = Bio::DB::IndexedBase->new('/path/to/file');
@@ -246,6 +245,7 @@ BEGIN {
}
use strict;
+use warnings;
use IO::File;
use AnyDBM_File;
use Fcntl;
@@ -264,49 +264,48 @@ use constant DNA => 1;
use constant RNA => 2;
use constant PROTEIN => 3;
+# You can avoid dying if you want but you may get incorrect results
use constant DIE_ON_MISSMATCHED_LINES => 1;
-# you can avoid dying if you want but you may get incorrect results
-
-
-# Compiling the below regular expressions speeds up the Pure Perl
-# seq/subseq() from Bio::DB::Fasta by about 7% from 7.76s to 7.22s
-# over 32358 calls on Variant Effect Prediction data.
-my $nl = qr/\n/;
-my $cr = qr/\r/;
# Remove carriage returns (\r) and newlines (\n) from a string. When
# called from subseq, this can take a signficiant portion of time, in
# Variant Effect Prediction. Therefore we compile the match portion.
sub _strip_crnl {
- my $str = shift;
- $str =~ s/$nl//g;
- $str =~ s/$cr//g;
- return $str;
-}
-
-# C can do perfrom _strip_crnl much faster. But this requires the
-# Inline::C module which we don't require people to have. So we make
-# this optional by wrapping the C code in an eval. If the eval works,
-# the Perl strip_crnl() function is overwritten.
-eval q{
- use Inline C => <<'END_OF_C_CODE';
- /* Strip all new line (\n) and carriage return (\r) characters
- from string str
- */
- char* _strip_crnl(char* str) {
- char *s;
- char *s2 = str;
- for (s = str; *s; *s++) {
+ eval 'require Inline::C';
+ if ( $INC{'Inline/C.pm'} ) {
+ # C can do _strip_crnl much faster. But this requires the
+ # Inline::C module which we don't require people to have. So we make
+ # this optional by wrapping the C code in an eval. If the eval works,
+ # the Perl strip_crnl() function is overwritten.
+ Inline->bind(
+ C => q(
+ /*
+ Strip all newlines (\n) and carriage returns (\r) from the string
+ */
+ char* _strip_crnl(char* str) {
+ char *s;
+ char *s2 = str;
+ for (s = str; *s; *s++) {
if (*s != '\n' && *s != '\r') {
*s2++ = *s;
}
+ }
+ *s2 = '\0';
+ return str;
}
- *s2 = '\0';
- return str;
+ )
+ );
+ } else {
+ # "tr" is much faster than the regex, with "s"
+ *Bio::DB::IndexedBase::_strip_crnl = sub {
+ my $str = shift;
+ $str =~ tr/\n\r//d;
+ return $str;
+ };
}
-END_OF_C_CODE
-};
+ return _strip_crnl(@_);
+}
=head2 new
@@ -393,7 +392,7 @@ sub new {
require Cwd;
$dirname = Cwd::getcwd();
} else {
- $self->{index_name} ||= $self->_default_index_name($path);
+ $self->{index_name} ||= $self->_default_index_name($path);
if (-d $path) {
# because Win32 glob() is broken with respect to long file names
# that contain whitespace.
@@ -505,7 +504,10 @@ sub get_all_primary_ids {
return keys %{shift->{offsets}};
}
+{
+no warnings 'once';
*ids = *get_all_ids = \&get_all_primary_ids;
+}
=head2 index_file
@@ -623,7 +625,10 @@ sub get_Seq_by_id {
return $self->{obj_class}->new($self, $id);
}
+{
+no warnings 'once';
*get_Seq_by_version = *get_Seq_by_primary_id = *get_Seq_by_acc = \&get_Seq_by_id;
+}
=head2 _calculate_offsets
@@ -835,8 +840,9 @@ sub _fh {
my ($self, $id) = @_;
$self->throw('Need to provide a sequence ID') if not defined $id;
my $file = $self->file($id) or return;
- return $self->_fhcache( File::Spec->catfile($self->{dirname}, $file) ) or
- $self->throw( "Can't open file $file");
+ return eval {
+ $self->_fhcache( File::Spec->catfile($self->{dirname}, $file));
+ } or $self->throw( "Can't open file $file" );
}
diff --git a/Bio/DB/LocationI.pm b/Bio/DB/LocationI.pm
index 5bc688e..857847f 100644
--- a/Bio/DB/LocationI.pm
+++ b/Bio/DB/LocationI.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::LocationI
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
@@ -15,7 +15,7 @@
Bio::DB::LocationI - A RandomAccessI-like abstract interface for
retrieving location data from a sequence database and returning
-Bio::LocationI objects
+Bio::LocationI objects
=head1 SYNOPSIS
@@ -32,7 +32,7 @@ Bio::LocationI objects
=head1 DESCRIPTION
This is a pure interface class - in other words, all this does is define
-methods which other (concrete) classes will actually implement.
+methods which other (concrete) classes will actually implement.
The Bio::DB::LocationI class defines methods used to retrieve location data
from a sequence. This is returned in the form of Bio::LocationI objects,
@@ -52,24 +52,24 @@ is based.
=head2 Mailing Lists
-User feedback is an integral part of the
+User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l at lists.open-bio.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -80,7 +80,7 @@ Bug reports can be submitted via the web.
https://github.com/bioperl/bioperl-live/issues
-=head1 AUTHOR
+=head1 AUTHOR
Email cjfields at bioperl dot org
diff --git a/Bio/DB/MeSH.pm b/Bio/DB/MeSH.pm
index 1e9bd65..767633e 100644
--- a/Bio/DB/MeSH.pm
+++ b/Bio/DB/MeSH.pm
@@ -184,7 +184,7 @@ sub _set_cgi_base_url {
Title : get_exact_term
Usage : $s = $db->get_exact_term($value);
- Function: Retrive a single MeSH term using a unique ID or exact name.
+ Function: Retrieve a single MeSH term using a unique ID or exact name.
Example :
Returns : a Bio::Phenotype::MeSH::Term object
Args : scalar, UID or name of a MeSH term
@@ -286,7 +286,7 @@ sub _run {
sub result {
my ($self,$value) = @_;
- $self->throw("Could not retrive results") unless $self->status('COMPLETED');
+ $self->throw("Could not retrieve results") unless $self->status('COMPLETED');
# no processing
return $self->{'_content'} if $value && $value eq 'raw';
diff --git a/Bio/DB/Qual.pm b/Bio/DB/Qual.pm
index 675b470..729d7bc 100644
--- a/Bio/DB/Qual.pm
+++ b/Bio/DB/Qual.pm
@@ -66,7 +66,7 @@ specific portion of the gi|gb|abc|xyz GenBank IDs.
=head1 DATABASE CREATION AND INDEXING
The object-oriented constructor is new(), the filehandle constructor is newFh()
-and the tied hash constructor is tie(). They all allow to index a single Fasta
+and the tied hash constructor is tie(). They all allow one to index a single Fasta
file, several files, or a directory of files. See Bio::DB::IndexedBase.
=head1 SEE ALSO
diff --git a/Bio/DB/Query/HIVQuery.pm b/Bio/DB/Query/HIVQuery.pm
index 64ec068..8e14209 100755
--- a/Bio/DB/Query/HIVQuery.pm
+++ b/Bio/DB/Query/HIVQuery.pm
@@ -590,7 +590,7 @@ sub remove_annotations {
Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
- Function: access the annotation value assocated with the given tags
+ Function: access the annotation value associated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree
diff --git a/Bio/DB/RefSeq.pm b/Bio/DB/RefSeq.pm
index 2b7ad4c..bc0acaf 100644
--- a/Bio/DB/RefSeq.pm
+++ b/Bio/DB/RefSeq.pm
@@ -41,7 +41,7 @@ Bio::DB::RefSeq - Database object interface for RefSeq retrieval
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
- # also don't want features, just sequence so let's save bandwith
+ # also don't want features, just sequence so let's save bandwidth
# and request Fasta sequence
$db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
-format => 'fasta');
@@ -65,7 +65,7 @@ The functionality of this module is inherited from L<Bio::DB::DBFetch>
which implements L<Bio::DB::WebDBSeqI>.
This module retrieves entries from EBI although it
-retrives database entries produced at NCBI. When read into bioperl
+retrieves database entries produced at NCBI. When read into bioperl
objects, the parser for GenBank format it used. RefSeq is a
NONSTANDARD GenBank file so be ready for surprises.
diff --git a/Bio/DB/ReferenceI.pm b/Bio/DB/ReferenceI.pm
index def8f90..de9a102 100644
--- a/Bio/DB/ReferenceI.pm
+++ b/Bio/DB/ReferenceI.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::ReferenceI
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
@@ -15,7 +15,7 @@
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for
retrieving Reference data from a sequence database and returning
-Bio::Annotation::Reference objects
+Bio::Annotation::Reference objects
=head1 SYNOPSIS
@@ -32,7 +32,7 @@ Bio::Annotation::Reference objects
=head1 DESCRIPTION
This is a pure interface class - in other words, all this does is define
-methods which other (concrete) classes will actually implement.
+methods which other (concrete) classes will actually implement.
The Bio::DB::ReferenceI class defines methods used to retrieve reference data
from a sequence. This is returned in the form of Bio::Annotation::Reference
@@ -48,24 +48,24 @@ is based.
=head2 Mailing Lists
-User feedback is an integral part of the
+User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l at lists.open-bio.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -76,7 +76,7 @@ Bug reports can be submitted via the web.
https://github.com/bioperl/bioperl-live/issues
-=head1 AUTHOR
+=head1 AUTHOR
Email cjfields at bioperl dot org
diff --git a/Bio/DB/Registry.pm b/Bio/DB/Registry.pm
index e92f9a9..c768e8b 100644
--- a/Bio/DB/Registry.pm
+++ b/Bio/DB/Registry.pm
@@ -21,33 +21,33 @@ Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
=head1 DESCRIPTION
This module provides access to the Open Bio Database Access (OBDA)
-scheme, which provides a single cross-language and cross-platform
-specification of how to get to databases. These databases may be
+scheme, which provides a single cross-language and cross-platform
+specification of how to get to databases. These databases may be
accessible through the Web, they may be BioSQL databases, or
they may be local, indexed flatfile databases.
-If the user or system administrator has not installed the default init
-file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics
-then creating the first Registry object copies the default settings from
-the www.open-bio.org. The Registry object will attempt to store these
+If the user or system administrator has not installed the default init
+file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics
+then creating the first Registry object copies the default settings from
+the www.open-bio.org. The Registry object will attempt to store these
settings in a new file, ${HOME}/.bioinformatics/seqdatabase.ini.
-Users can specify one or more custom locations for the init file by
-setting $OBDA_SEARCH_PATH to those directories, where multiple
+Users can specify one or more custom locations for the init file by
+setting $OBDA_SEARCH_PATH to those directories, where multiple
directories should be separated by ';'.
Please see the OBDA Access HOWTO for more information
-(L<http://bioperl.open-bio.org/wiki/HOWTO:OBDA>).
+(L<http://bioperl.org/howtos/OBDA_HOWTO.html>).
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -70,7 +70,7 @@ methods. Internal methods are usually preceded with a _
package Bio::DB::Registry;
use vars qw($OBDA_SPEC_VERSION $OBDA_SEARCH_PATH
- $HOME $PRIVATE_DIR $PUBLIC_DIR $REGISTRY
+ $HOME $PRIVATE_DIR $PUBLIC_DIR $REGISTRY
$FALLBACK_REGISTRY);
use strict;
@@ -174,7 +174,7 @@ sub _load_registry {
} else {
eval {
my $randi = $class->new_from_registry( %{$hash->{$db}} );
- $self->{'_dbs'}->{$db}->add_database($randi);
+ $self->{'_dbs'}->{$db}->add_database($randi);
};
if ($@) {
$self->warn("Couldn't call new_from_registry() on [$class]\n$@");
@@ -246,7 +246,7 @@ sub _get_ini_files {
push @ini_files,$file;
}
}
- push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY"
+ push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY"
if ( $HOME && -e "$HOME/$PRIVATE_DIR/$REGISTRY" );
push @ini_files, "$PUBLIC_DIR/$REGISTRY"
if ( -e "$PUBLIC_DIR/$REGISTRY" );
@@ -267,11 +267,11 @@ sub _make_private_registry {
my $self = shift;
my @ini_file;
- my $nor_in = $OBDA_SEARCH_PATH ?
- "nor in directory specified by\n$OBDA_SEARCH_PATH" :
+ my $nor_in = $OBDA_SEARCH_PATH ?
+ "nor in directory specified by\n$OBDA_SEARCH_PATH" :
"and environment variable OBDA_SEARCH_PATH wasn't set";
- $self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" .
+ $self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" .
"nor in $PUBLIC_DIR $nor_in.\n" .
"Using web to get registry from\n$FALLBACK_REGISTRY");
diff --git a/Bio/DB/SeqFeature/Store.pm b/Bio/DB/SeqFeature/Store.pm
index fcf11ff..031c0ac 100644
--- a/Bio/DB/SeqFeature/Store.pm
+++ b/Bio/DB/SeqFeature/Store.pm
@@ -2620,7 +2620,7 @@ you want to calculate the coverage density. An object is returned
corresponding to the requested region. It contains a tag called
"coverage" that will return an array ref of "bins" length. Each
element of the array describes the number of features that overlap the
-bin at this postion.
+bin at this position.
Arguments:
diff --git a/Bio/DB/SeqFeature/Store/DBI/SQLite.pm b/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
index 846cb75..2d0d070 100644
--- a/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
@@ -436,7 +436,7 @@ sub _create_attribute_fts{
$dbh->do("CREATE VIRTUAL TABLE "
. $self->_attribute_table
. " USING " . $fts_versions[-1]
- . "(id integer not null, attribute_id integer not null, attribute_value text)");
+ . "(id, attribute_id, attribute_value)");
}
}
diff --git a/Bio/DB/SeqFeature/Store/GFF2Loader.pm b/Bio/DB/SeqFeature/Store/GFF2Loader.pm
index 174f8d0..6c97025 100644
--- a/Bio/DB/SeqFeature/Store/GFF2Loader.pm
+++ b/Bio/DB/SeqFeature/Store/GFF2Loader.pm
@@ -196,7 +196,7 @@ The following read-only accessors return values passed or created during new():
=head2 Internal Methods
-The following methods are used internally and may be overidden by
+The following methods are used internally and may be overridden by
subclasses.
=over 4
diff --git a/Bio/DB/SeqFeature/Store/GFF3Loader.pm b/Bio/DB/SeqFeature/Store/GFF3Loader.pm
index b8dc956..c149528 100644
--- a/Bio/DB/SeqFeature/Store/GFF3Loader.pm
+++ b/Bio/DB/SeqFeature/Store/GFF3Loader.pm
@@ -70,6 +70,7 @@ use strict;
use Carp 'croak';
use Bio::DB::GFF::Util::Rearrange;
use Bio::DB::SeqFeature::Store::LoadHelper;
+use constant DEBUG => 0;
use base 'Bio::DB::SeqFeature::Store::Loader';
@@ -262,7 +263,7 @@ The following read-only accessors return values passed or created during new():
=head2 Internal Methods
-The following methods are used internally and may be overidden by
+The following methods are used internally and may be overridden by
subclasses.
=over 4
@@ -555,7 +556,8 @@ sub handle_feature { #overridden
$feature_id = '' unless defined $feature_id;
$name = '' unless defined $name; # prevent uninit variable warnings
# push @{$unreserved->{Alias}},$feature_id if $has_loadid && $feature_id ne $name;
- $unreserved->{parent_id} = \@parent_ids if @parent_ids;
+ # If DEBUG != 0, any Parent attribute is also copied over (as 'parent_id')
+ $unreserved->{parent_id} = \@parent_ids if DEBUG && @parent_ids;
# POSSIBLY A PERMANENT HACK -- TARGETS BECOME ALIASES
# THIS IS TO ALLOW FOR TARGET-BASED LOOKUPS
diff --git a/Bio/DB/SeqFeature/Store/Loader.pm b/Bio/DB/SeqFeature/Store/Loader.pm
index 33b6a05..a47cd97 100644
--- a/Bio/DB/SeqFeature/Store/Loader.pm
+++ b/Bio/DB/SeqFeature/Store/Loader.pm
@@ -284,7 +284,7 @@ sub verbose { shift->{verbose} }
=head2 Internal Methods
-The following methods are used internally and may be overidden by
+The following methods are used internally and may be overridden by
subclasses.
=over 4
diff --git a/Bio/DB/TFBS/transfac_pro.pm b/Bio/DB/TFBS/transfac_pro.pm
index 1883685..3e36583 100644
--- a/Bio/DB/TFBS/transfac_pro.pm
+++ b/Bio/DB/TFBS/transfac_pro.pm
@@ -363,7 +363,7 @@ sub get_fragment {
Function: Get a matrix that describes a binding site.
Returns : Bio::Matrix::PSM::SiteMatrix
Args : string - a matrix id ('M...'), optionally a sequence string from
- which base frequencies will be calcualted for the matrix model
+ which base frequencies will be calculated for the matrix model
(default 0.25 each)
=cut
@@ -781,7 +781,7 @@ sub _build_index {
my ($self, $dat_dir, $force) = @_;
# MLDBM would give us transparent complex data structures with DB_File,
- # allowing just one index file, but its yet another requirment and we
+ # allowing just one index file, but its yet another requirement and we
# don't strictly need it
my $index_dir = $self->index_directory;
@@ -1740,7 +1740,7 @@ sub _db_connect {
=head2 index_directory
Title : index_directory
- Funtion : Get/set the location that index files are stored. (this module
+ Function : Get/set the location that index files are stored. (this module
will index the supplied database)
Usage : $obj->index_directory($newval)
Returns : value of index_directory (a scalar)
@@ -1789,7 +1789,7 @@ sub _species_to_taxid {
}
}
else {
- # some species lines are poorly formated so custom handling
+ # some species lines are poorly formatted so custom handling
SWITCH: for ($raw_species) {
# for speed, go by common first letters
my $first_letter = substr($raw_species, 0, 1);
diff --git a/Bio/DB/Taxonomy/entrez.pm b/Bio/DB/Taxonomy/entrez.pm
index 67d255f..b4644d1 100644
--- a/Bio/DB/Taxonomy/entrez.pm
+++ b/Bio/DB/Taxonomy/entrez.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::Taxonomy::entrez
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
@@ -34,8 +34,8 @@ Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver
print "family is $family\n";
# Can also go up 4 levels
- my $p = $node;
- for ( 1..4 ) {
+ my $p = $node;
+ for ( 1..4 ) {
$p = $db->get_Taxonomy_Node(-taxonid => $p->parent_id);
}
print $p->rank, " ", ($p->classification)[0], "\n";
@@ -64,15 +64,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -126,7 +126,7 @@ $EntrezSummary = 'esummary.fcgi';
$DATA_CACHE = {};
$RELATIONS = {};
-%EntrezParams = ( 'db' => 'taxonomy',
+%EntrezParams = ( 'db' => 'taxonomy',
'report' => 'xml',
'retmode'=> 'xml',
'tool' => 'Bioperl');
@@ -152,10 +152,10 @@ $UrlParamSeparatorValue = '&';
sub new {
my ($class, @args) = @_;
-
+
# need to initialise Bio::WebAgent...
my ($self) = $class->SUPER::new(@args);
-
+
# ... as well as our normal Bio::DB::Taxonomy selves:
$self->_initialize(@args);
return $self;
@@ -200,7 +200,7 @@ sub get_num_taxa {
# and the total number is reported as well (which is what we are interested
# in).
my %p = $self->entrez_params;
- $p{'term'} = 'all[Filter]';
+ $p{'term'} = 'all[Filter]';
my $twig = $self->_run_query($self->_build_url($EntrezGet, \%p));
my $count = $twig->root->first_child('Count')->first_child->text;
return $count;
@@ -216,7 +216,7 @@ sub get_num_taxa {
Args : just a single value which is the database id, OR named args:
-taxonid => taxonomy id (to query by taxonid)
OR
- -name => string (to query by a taxonomy name: common name,
+ -name => string (to query by a taxonomy name: common name,
scientific name, etc)
OR
To retrieve a taxonomy node for a GI number provide the -gi option
@@ -252,10 +252,10 @@ sub get_taxon {
# the call based on the TaxId
my %p = %SequenceParams;
my %items;
- if( ref($params{'-gi'}) =~ /ARRAY/i ) {
+ if( ref($params{'-gi'}) =~ /ARRAY/i ) {
$p{'id'} = join(',', @{$params{'-gi'}});
- } else {
- $p{'id'} = $params{'-gi'};
+ } else {
+ $p{'id'} = $params{'-gi'};
}
$p{'db'} = $db if defined $db;
my $url = $self->_build_url($EntrezSummary, \%p);
@@ -265,7 +265,7 @@ sub get_taxon {
}
else {
my $twig = $self->_run_query($url);
- my $root = $twig->root;
+ my $root = $twig->root;
for my $topnode ( $root->children('DocSum') ) {
for my $child ( $topnode->children('Item') ) {
if( uc($child->{att}->{'Name'}) eq 'TAXID' ) {
@@ -273,19 +273,19 @@ sub get_taxon {
}
}
}
-
+
$DATA_CACHE->{gi_to_ids}->{$url} = \@ids;
}
-
+
return $self->get_taxon(-taxonid => \@ids);
}
elsif ($params{'-name'}) {
@taxonids = $self->get_taxonid($params{'-name'});
}
- else {
+ else {
$self->warn("Need to have provided either a -taxonid or -name value to get_taxon");
}
-
+
if ($params{'-full'}) {
$want_full = 1;
}
@@ -293,14 +293,14 @@ sub get_taxon {
else {
$taxonid = shift;
}
-
+
if (ref($taxonid) =~ /ARRAY/i ) {
@taxonids = @{$taxonid};
}
else {
push(@taxonids, $taxonid) if $taxonid;
}
-
+
# return answer(s) from the cache if possible
my @results;
my @uncached;
@@ -316,10 +316,10 @@ sub get_taxon {
push(@uncached, $taxonid);
}
}
-
+
if (@uncached > 0) {
$taxonid = join(',', @uncached);
-
+
$p{'id'} = $taxonid;
my $twig = $self->_run_query($self->_build_url($EntrezFetch, \%p));
@@ -327,15 +327,15 @@ sub get_taxon {
for my $taxon ( $root->children('Taxon') ) {
my $taxid = $taxon->first_child_text('TaxId');
$self->throw("Got a result with no TaxId!") unless $taxid;
-
+
my $data = {};
if (exists $DATA_CACHE->{minimal_info}->{$taxid}) {
$data = $DATA_CACHE->{minimal_info}->{$taxid};
}
-
+
$data->{id} = $taxid;
$data->{rank} = $taxon->first_child_text('Rank');
-
+
my $other_names = $taxon->first_child('OtherNames');
my @other_names = $other_names->children_text() if $other_names;
my $sci_name = $taxon->first_child_text('ScientificName');
@@ -344,14 +344,14 @@ sub get_taxon {
push(@other_names, $orig_sci_name) if $orig_sci_name ne $sci_name;
$data->{scientific_name} = $sci_name;
$data->{common_names} = \@other_names;
-
+
$data->{division} = $taxon->first_child_text('Division');
$data->{genetic_code} = $taxon->first_child('GeneticCode')->first_child_text('GCId');
$data->{mitochondrial_genetic_code} = $taxon->first_child('MitoGeneticCode')->first_child_text('MGCId');
$data->{create_date} = $taxon->first_child_text('CreateDate');
$data->{update_date} = $taxon->first_child_text('UpdateDate');
$data->{pub_date} = $taxon->first_child_text('PubDate');
-
+
# since we have some information about all the ancestors of our
# requested node, we may as well cache data for the ancestors to
# reduce the number of accesses to website in future
@@ -360,7 +360,7 @@ sub get_taxon {
my ($ancestor, $lineage_data, @taxa);
foreach my $lineage_taxon ($lineage_ex->children) {
my $lineage_taxid = $lineage_taxon->first_child_text('TaxId');
-
+
if (exists $DATA_CACHE->{minimal_info}->{$lineage_taxid} || exists $DATA_CACHE->{full_info}->{$lineage_taxid}) {
$lineage_data = $DATA_CACHE->{minimal_info}->{$lineage_taxid} || $DATA_CACHE->{full_info}->{$lineage_taxid};
next;
@@ -368,16 +368,16 @@ sub get_taxon {
else {
$lineage_data = {};
}
-
+
$lineage_data->{id} = $lineage_taxid;
$lineage_data->{scientific_name} = $lineage_taxon->first_child_text('ScientificName');
$lineage_data->{rank} = $lineage_taxon->first_child_text('Rank');
-
+
$RELATIONS->{ancestors}->{$lineage_taxid} = $ancestor->{id} if $ancestor;
-
+
$DATA_CACHE->{minimal_info}->{$lineage_taxid} = $lineage_data;
} continue { $ancestor = $lineage_data; unshift(@taxa, $lineage_data); }
-
+
$RELATIONS->{ancestors}->{$taxid} = $ancestor->{id} if $ancestor;
# go through the lineage in reverse so we can remember the children
@@ -392,7 +392,7 @@ sub get_taxon {
push(@results, $self->_make_taxon($data));
}
}
-
+
wantarray() ? @results : shift @results;
}
@@ -414,7 +414,7 @@ sub get_taxon {
sub get_taxonids {
my ($self,$query) = @_;
my %p = $self->entrez_params;
-
+
# queries don't work correctly with special characters, so get rid of them.
if ($query =~ /<.+>/) {
# queries with <something> will fail, so workaround by removing, doing
@@ -423,10 +423,10 @@ sub get_taxonids {
# case-insensitive matching to the word(s) within <>
$query =~ s/ <(.+?)>//;
my $desired_parent_name = lc($1);
-
- ID: foreach my $start_id ($self->get_taxonids($query)) {
+
+ ID: for my $start_id ($self->get_taxonids($query)) {
my $node = $self->get_taxon($start_id) || next ID;
-
+
# walk up the parents until we hit a node with a named rank
while (1) {
my $parent_node = $self->ancestor($node) || next ID;
@@ -437,13 +437,13 @@ sub get_taxonids {
$parent_node = $self->get_taxon(-taxonid => $parent_node->id, -full => 1);
@parent_common_names = $parent_node->common_names;
}
-
- foreach my $name ($parent_sci_name, @parent_common_names) {
+
+ for my $name ($parent_sci_name, @parent_common_names) {
if (lc($name) eq $desired_parent_name) {
return wantarray() ? ($start_id) : $start_id;
}
}
-
+
my $parent_rank = $parent_node->rank || 'no rank';
if ($parent_rank ne 'no rank') {
last;
@@ -455,9 +455,9 @@ sub get_taxonids {
}
return;
}
- $query =~ s/[\"\(\)]//g; # not an exhaustive list; these are just the ones I know cause problems
+ $query =~ s/[\"\(\)]//g; # not an exhaustive list; these are just the ones we know cause problems
$query =~ s/\s/+/g;
-
+
my @data;
if (defined $DATA_CACHE->{name_to_id}->{$query}) {
@data = @{$DATA_CACHE->{name_to_id}->{$query}};
@@ -467,12 +467,26 @@ sub get_taxonids {
my $twig = $self->_run_query($self->_build_url($EntrezGet, \%p));
my $root = $twig->root;
+
+ # Check that all words in the query are found, because we do not want to
+ # match just 1 word if there are multiple words, e.g. if we query with
+ # "Homo sapiens" both "homo" and "sapiens" must be found
+ my $errorlist = $root->first_child('ErrorList');
+ if ( $errorlist ) {
+ my @notfound = map { $_->text } $errorlist->children('PhraseNotFound');
+ if ( @notfound ) {
+ for my $term ( @notfound ) {
+ return "No hit" if $query =~ /$term/;
+ }
+ }
+ }
+
my $list = $root->first_child('IdList');
@data = map { $_->text } $list->children('Id');
-
+
$DATA_CACHE->{name_to_id}->{$query} = [@data];
}
-
+
return wantarray() ? @data : shift @data;
}
@@ -499,7 +513,7 @@ sub ancestor {
$self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
$self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self;
my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!");
-
+
my $ancestor_id = $RELATIONS->{ancestors}->{$id} || return;
return $self->_make_taxon($DATA_CACHE->{full_info}->{$ancestor_id} || $DATA_CACHE->{minimal_info}->{$ancestor_id});
}
@@ -526,13 +540,13 @@ sub each_Descendent {
$self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
$self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self;
my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!");
-
+
my @children_ids = keys %{$RELATIONS->{children}->{$id} || {}};
my @children;
foreach my $child_id (@children_ids) {
push(@children, $self->_make_taxon($DATA_CACHE->{full_info}->{$child_id} || $DATA_CACHE->{minimal_info}->{$child_id}));
}
-
+
return @children;
}
@@ -615,9 +629,9 @@ sub entrez_params{
# make a Taxon object from data hash ref
sub _make_taxon {
my ($self, $data) = @_;
-
+
my $taxon = Bio::Taxon->new();
-
+
my $taxid;
while (my ($method, $value) = each %{$data}) {
if ($method eq 'id') {
@@ -626,13 +640,13 @@ sub _make_taxon {
}
$taxon->$method(ref($value) eq 'ARRAY' ? @{$value} : $value);
}
-
+
# we can't use -dbh or the db_handle() method ourselves or we'll go
# infinite on the merge attempt
$taxon->{'db_handle'} = $self;
-
+
$self->_handle_internal_id($taxon);
-
+
return $taxon;
}
diff --git a/Bio/DB/Taxonomy/flatfile.pm b/Bio/DB/Taxonomy/flatfile.pm
index ab2e13a..677b039 100644
--- a/Bio/DB/Taxonomy/flatfile.pm
+++ b/Bio/DB/Taxonomy/flatfile.pm
@@ -506,7 +506,7 @@ sub _db_connect {
=head2 index_directory
Title : index_directory
- Funtion : Get/set the location that index files are stored. (this module
+ Function : Get/set the location that index files are stored. (this module
will index the supplied database)
Usage : $obj->index_directory($newval)
Returns : value of index_directory (a scalar)
diff --git a/Bio/DB/Taxonomy/sqlite.pm b/Bio/DB/Taxonomy/sqlite.pm
index a0e2411..4bf6ca1 100644
--- a/Bio/DB/Taxonomy/sqlite.pm
+++ b/Bio/DB/Taxonomy/sqlite.pm
@@ -460,7 +460,7 @@ SQL
=head2 index_directory
Title : index_directory
- Funtion : Get/set the location that index files are stored. (this module
+ Function : Get/set the location that index files are stored. (this module
will index the supplied database)
Usage : $obj->index_directory($newval)
Returns : value of index_directory (a scalar)
@@ -478,7 +478,7 @@ sub index_directory {
=head2 db_name
Title : db_name
- Funtion : Get/set the name of the SQLite3 database where data is stored
+ Function : Get/set the name of the SQLite3 database where data is stored
Usage : $obj->db_name($newval)
Returns : value of db_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
@@ -498,7 +498,7 @@ sub db_name {
=head2 cache_size
Title : cache_size
- Funtion : Get/set the cachesize used for loading the SQLite3 database
+ Function : Get/set the cachesize used for loading the SQLite3 database
Usage : $obj->cache_size($newval)
Returns : value of cache_size (a scalar)
Args : on set, new value (a scalar or undef, optional)
diff --git a/Bio/DB/WebDBSeqI.pm b/Bio/DB/WebDBSeqI.pm
index e83110f..eff5189 100644
--- a/Bio/DB/WebDBSeqI.pm
+++ b/Bio/DB/WebDBSeqI.pm
@@ -26,7 +26,7 @@ for retrieving sequences
=head1 DESCRIPTION
Provides core set of functionality for connecting to a web based
-database for retriving sequences.
+database for retrieving sequences.
Users wishing to add another Web Based Sequence Dabatase will need to
extend this class (see L<Bio::DB::SwissProt> or L<Bio::DB::NCBIHelper> for
@@ -344,7 +344,7 @@ sub get_Stream_by_gi {
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of accession.version strings for
the desired sequence entries
- Note : For GenBank, this is implemeted in NCBIHelper
+ Note : For GenBank, this is implemented in NCBIHelper
=cut
diff --git a/Bio/DescribableI.pm b/Bio/DescribableI.pm
index 51911f3..09247cc 100644
--- a/Bio/DescribableI.pm
+++ b/Bio/DescribableI.pm
@@ -80,7 +80,7 @@ define.
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
- user of this interface would not assumme this) and should be
+ user of this interface would not assume this) and should be
less than thirty characters (though again, double checking
this is a good idea)
Returns : A scalar
diff --git a/Bio/Factory/ApplicationFactoryI.pm b/Bio/Factory/ApplicationFactoryI.pm
index 15e5580..5dad006 100644
--- a/Bio/Factory/ApplicationFactoryI.pm
+++ b/Bio/Factory/ApplicationFactoryI.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::Factory::ApplicationFactoryI
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
@@ -17,7 +17,7 @@ Bio::Factory::ApplicationFactoryI - Interface class for Application Factories
=head1 SYNOPSIS
-You wont be using this as an object, but using a derived class.
+You won't be using this as an object, but using a derived class.
=head1 DESCRIPTION
@@ -34,15 +34,15 @@ Bioperl mailing lists Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
diff --git a/Bio/Factory/ObjectFactoryI.pm b/Bio/Factory/ObjectFactoryI.pm
index 758cae1..e1b5ea3 100644
--- a/Bio/Factory/ObjectFactoryI.pm
+++ b/Bio/Factory/ObjectFactoryI.pm
@@ -101,7 +101,7 @@ sub create{
Usage : $obj = $factory->create_object(%args)
Function: Create a new object.
- This is supposed to supercede create(). Right now it only delegates
+ This is supposed to supersede create(). Right now it only delegates
to create().
Returns : a new object
Args : hash of initialization parameters
diff --git a/Bio/Index/Abstract.pm b/Bio/Index/Abstract.pm
index 13b7511..6ad2ba8 100644
--- a/Bio/Index/Abstract.pm
+++ b/Bio/Index/Abstract.pm
@@ -2,7 +2,7 @@
#
# BioPerl module for Bio::Index::Abstract
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Ewan Birney <birney at sanger.ac.uk>
# and James Gilbert <jgrg at sanger.ac.uk>
@@ -48,15 +48,15 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -119,7 +119,7 @@ BEGIN {
-dbm_package => 'DB_File',
-verbose => 0);
Function: Returns a new index object. If filename is
- specified, then open_dbm() is immediately called.
+ specified, then open_dbm() is immediately called.
Bio::Index::Abstract->new() will usually be called
directly only when opening an existing index.
Returns : A new index object
@@ -137,7 +137,7 @@ sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my( $filename, $write_flag, $dbm_package, $cachesize, $ffactor, $pathtype ) =
- $self->_rearrange([qw(FILENAME
+ $self->_rearrange([qw(FILENAME
WRITE_FLAG
DBM_PACKAGE
CACHESIZE
@@ -181,7 +181,7 @@ sub new {
Usage : $value = $self->write_flag();
$self->write_flag($value);
Function: Gets or sets the value of write_flag, which
- is wether the dbm file should be opened with
+ is whether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
@@ -192,11 +192,11 @@ sub new {
Usage : $value = $self->dbm_package();
$self->dbm_package($value);
- Function: Gets or sets the name of the Perl dbm module used.
+ Function: Gets or sets the name of the Perl dbm module used.
If the value is unset, then it returns the value of
the package variable $USE_DBM_TYPE or if that is
unset, then it chooses the best available dbm type,
- choosing 'DB_File' in preference to 'SDBM_File'.
+ choosing 'DB_File' in preference to 'SDBM_File'.
Bio::Abstract::Index may work with other dbm file
types.
@@ -257,10 +257,10 @@ sub db {
at the approprite place
This provides for a way to get the actual
- file contents and not an object
+ file contents and not an object
WARNING: you must parse the record deliminter
- *yourself*. Abstract wont do this for you
+ *yourself*. Abstract won't do this for you
So this code
$fh = $index->get_stream($myid);
@@ -277,7 +277,7 @@ sub db {
Returns : A filehandle object
Args : string represents the accession number
- Notes : This method should not be used without forethought
+ Notes : This method should not be used without forethought
=cut
@@ -355,7 +355,7 @@ sub ffactor {
object. Write access is only given if explicitly
asked for by calling new(-write => 1) or having set
the write_flag(1) on the index object. The type of
- dbm file opened is that returned by dbm_package().
+ dbm file opened is that returned by dbm_package().
The name of the file to be is opened is obtained by
calling the filename() method.
@@ -383,7 +383,7 @@ sub open_dbm {
# Choose mode for opening dbm file (read/write+create or read-only).
my $mode_flags = $self->write_flag ? O_RDWR|O_CREAT : O_RDONLY;
-
+
# Open the dbm file
if ($dbm_type eq 'DB_File') {
my $hash_inf = DB_File::HASHINFO->new();
@@ -406,7 +406,7 @@ sub open_dbm {
# Now, if we're a Bio::Index::Abstract caterpillar, then we
# transform ourselves into a Bio::Index::<something> butterfly!
- if( ref($self) eq "Bio::Index::Abstract" ) {
+ if( ref($self) eq "Bio::Index::Abstract" ) {
my $pkg = $self->_code_base();
bless $self, $pkg;
}
@@ -428,8 +428,8 @@ sub open_dbm {
index module. Used to permanently identify an index
file as having been created by a particular version
of the index module. Must be provided by the sub class
- Example :
- Returns :
+ Example :
+ Returns :
Args : none
=cut
@@ -445,7 +445,7 @@ sub _version {
Usage : $code = $db->_code_base();
Function:
Example :
- Returns : Code package to be used with this
+ Returns : Code package to be used with this
Args :
@@ -475,7 +475,7 @@ sub _code_base {
module and version of that module that made it. If the
index is empty, then it adds the information to the
database.
- Example :
+ Example :
Returns : 1 or exception
Args : none
@@ -510,9 +510,9 @@ sub _type_and_version {
are the same size as when the database was built,
or throws an exception. Called by the new()
function.
- Example :
+ Example :
Returns : 1 or exception
- Args :
+ Args :
=cut
@@ -567,11 +567,11 @@ sub make_index {
}
} else {
if( $^O =~ /MSWin/i ) {
- ($files[$i] =~ m|^[A-Za-z]:/|) ||
+ ($files[$i] =~ m|^[A-Za-z]:/|) ||
$self->throw("Not an absolute file path '$files[$i]'");
} else {
- ($files[$i] =~ m|^/|) ||
- $self->throw("Not an absolute file path '$files[$i]'");
+ ($files[$i] =~ m|^/|) ||
+ $self->throw("Not an absolute file path '$files[$i]'");
}
}
$self->throw("File does not exist '$files[$i]'") unless -e $files[$i];
@@ -596,9 +596,9 @@ sub make_index {
if( ($record = $self->db->{"__FILENAME_$file"}) ) {
($number,$size) = $self->unpack_record($record);
- # if it is the same size - fine. Otherwise die
+ # if it is the same size - fine. Otherwise die
if( -s $file == $size ) {
- $self->warn("File $file already indexed. Skipping...");
+ $self->warn("File $file already indexed. Skipping...");
next FILE;
} else {
$self->throw("In index, $file has changed size ($size). Indicates that the index is out of date");
@@ -653,7 +653,7 @@ sub pathtype {
$self->throw("Type of path can only be 'relative' or 'absolute', not [$type].");
}
$self->{'_filepathtype'} = $type;
- }
+ }
return $self->{'_filepathtype'};
}
@@ -664,9 +664,9 @@ sub pathtype {
Title : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=cut
@@ -716,7 +716,7 @@ sub _file_handle {
track the number of files indexed. Sets or gets
the number of files indexed when called with or
without an argument.
- Example :
+ Example :
Returns : INT
Args : INT
@@ -763,7 +763,7 @@ sub add_record {
Usage : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
joined by ASCII 034 (which is unlikely to be used
- in any of the strings), and returns it.
+ in any of the strings), and returns it.
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args : LIST
@@ -801,7 +801,7 @@ sub unpack_record {
Title : count_records
Usage : $recs = $seqdb->count_records()
- Function: return count of all recs in the index
+ Function: return count of all recs in the index
Example :
Returns : a scalar
Args : none
diff --git a/Bio/Index/AbstractSeq.pm b/Bio/Index/AbstractSeq.pm
index 7dcb93a..d1cfd0d 100644
--- a/Bio/Index/AbstractSeq.pm
+++ b/Bio/Index/AbstractSeq.pm
@@ -146,7 +146,7 @@ sub fetch {
$seq = $seqio->next_seq();
}
- # we essentially assumme that the primary_id for the database
+ # we essentially assume that the primary_id for the database
# is the display_id
if (ref($seq) && $seq->isa('Bio::PrimarySeqI') &&
$seq->primary_id =~ /^\D+$/) {
diff --git a/Bio/Index/Blast.pm b/Bio/Index/Blast.pm
index 84bd2d0..77f1cf2 100644
--- a/Bio/Index/Blast.pm
+++ b/Bio/Index/Blast.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::Index::Blast
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Jason Stajich <jason at bioperl.org>
#
@@ -13,7 +13,7 @@
=head1 NAME
-Bio::Index::Blast - Indexes Blast reports and supports retrieval
+Bio::Index::Blast - Indexes Blast reports and supports retrieval
based on query accession(s)
=head1 SYNOPSIS
@@ -72,15 +72,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -124,7 +124,7 @@ sub _version {
-verbose => 0);
Function: Returns a new index object. If filename is
- specified, then open_dbm() is immediately called.
+ specified, then open_dbm() is immediately called.
Bio::Index::Abstract->new() will usually be called
directly only when opening an existing index.
Returns : A new index object
@@ -154,7 +154,7 @@ sub new {
Title : fetch_report
Usage : my $blastreport = $idx->fetch_report($id);
- Function: Returns a Bio::SearchIO report object
+ Function: Returns a Bio::SearchIO report object
for a specific blast report
Returns : Bio::SearchIO
Args : valid id
@@ -174,7 +174,7 @@ sub fetch_report{
Title : fetch_result
Usage : my $blastreport = $idx->fetch_result($id);
- Function: Returns a Bio::SearchIO report object
+ Function: Returns a Bio::SearchIO report object
for a specific blast report
Returns : Bio::SearchIO
Args : valid id
@@ -195,9 +195,9 @@ sub fetch_report{
Function: Specialist function to index BLAST report file(s).
Is provided with a filename and an integer
by make_index in its SUPER class.
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=cut
@@ -260,7 +260,7 @@ sub _index_file {
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
- parser for different flavours of blast dbs.
+ parser for different flavours of blast dbs.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
@@ -304,15 +304,15 @@ sub default_id_parser {
=head2 blast_parser_type
Title : blast_parser_type
- Usage : $index->blast_parser_type() # returns
+ Usage : $index->blast_parser_type() # returns
Function: Get/Set SearchIO-based text (-m0) BLAST parser. Only values in
local %VALID_PARSERS hash allowed.
Returns : String
- Args : [optional]
+ Args : [optional]
Note : This only allows simple text-based parsing options; tabular, XML,
or others are not supported (see Bio::Index::BlastTable for tab
output).
-
+
=cut
my %VALID_PARSERS = map {$_ =>1} qw(blast blast_pull);
@@ -347,7 +347,7 @@ sub blast_parser_type {
Usage : $value = $self->write_flag();
$self->write_flag($value);
Function: Gets or sets the value of write_flag, which
- is wether the dbm file should be opened with
+ is whether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
@@ -358,11 +358,11 @@ sub blast_parser_type {
Usage : $value = $self->dbm_package();
$self->dbm_package($value);
- Function: Gets or sets the name of the Perl dbm module used.
+ Function: Gets or sets the name of the Perl dbm module used.
If the value is unset, then it returns the value of
the package variable $USE_DBM_TYPE or if that is
unset, then it chooses the best available dbm type,
- choosing 'DB_File' in preference to 'SDBM_File'.
+ choosing 'DB_File' in preference to 'SDBM_File'.
Bio::Abstract::Index may work with other dbm file
types.
@@ -379,10 +379,10 @@ sub blast_parser_type {
at the approprite place
This provides for a way to get the actual
- file contents and not an object
+ file contents and not an object
WARNING: you must parse the record deliminter
- *yourself*. Abstract wont do this for you
+ *yourself*. Abstract won't do this for you
So this code
$fh = $index->get_stream($myid);
@@ -399,7 +399,7 @@ sub blast_parser_type {
Returns : A filehandle object
Args : string represents the accession number
- Notes : This method should not be used without forethought
+ Notes : This method should not be used without forethought
=head2 open_dbm
@@ -409,7 +409,7 @@ sub blast_parser_type {
object. Write access is only given if explicitly
asked for by calling new(-write => 1) or having set
the write_flag(1) on the index object. The type of
- dbm file opened is that returned by dbm_package().
+ dbm file opened is that returned by dbm_package().
The name of the file to be is opened is obtained by
calling the filename() method.
@@ -425,8 +425,8 @@ sub blast_parser_type {
index module. Used to permanently identify an index
file as having been created by a particular version
of the index module. Must be provided by the sub class
- Example :
- Returns :
+ Example :
+ Returns :
Args : none
=head2 _filename
@@ -434,9 +434,9 @@ sub blast_parser_type {
Title : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=head2 _file_handle
@@ -459,7 +459,7 @@ sub blast_parser_type {
track the number of files indexed. Sets or gets
the number of files indexed when called with or
without an argument.
- Example :
+ Example :
Returns : INT
Args : INT
@@ -483,7 +483,7 @@ sub blast_parser_type {
Usage : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
joined by ASCII 034 (which is unlikely to be used
- in any of the strings), and returns it.
+ in any of the strings), and returns it.
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args : LIST
diff --git a/Bio/Index/BlastTable.pm b/Bio/Index/BlastTable.pm
index 9d19d69..a531ccb 100644
--- a/Bio/Index/BlastTable.pm
+++ b/Bio/Index/BlastTable.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::Index::BlastTable
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Chris Fields <cjfields at uiuc.edu>
#
@@ -70,15 +70,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -122,7 +122,7 @@ sub _version {
-verbose => 0);
Function: Returns a new index object. If filename is
- specified, then open_dbm() is immediately called.
+ specified, then open_dbm() is immediately called.
Bio::Index::Abstract->new() will usually be called
directly only when opening an existing index.
Returns : A new index object
@@ -149,7 +149,7 @@ sub new {
Title : fetch_report
Usage : my $blastreport = $idx->fetch_report($id);
- Function: Returns a Bio::SearchIO report object
+ Function: Returns a Bio::SearchIO report object
for a specific blast report
Returns : Bio::SearchIO
Args : valid id
@@ -177,9 +177,9 @@ sub fetch_report{
Function: Specialist function to index BLAST report file(s).
Is provided with a filename and an integer
by make_index in its SUPER class.
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=cut
@@ -213,7 +213,7 @@ sub _index_file {
}
next
}
-
+
if (/^(?:([^\t]+)\t)(?:[^\t]+\t){7,}/) {
next if $last_query eq $1;
$indexpoint = tell($BLAST) - length($_) - $correction unless $is_m9;
@@ -235,7 +235,7 @@ sub _index_file {
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
- parser for different flavours of blast dbs.
+ parser for different flavours of blast dbs.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
@@ -297,7 +297,7 @@ sub default_id_parser
Usage : $value = $self->write_flag();
$self->write_flag($value);
Function: Gets or sets the value of write_flag, which
- is wether the dbm file should be opened with
+ is whether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
@@ -308,11 +308,11 @@ sub default_id_parser
Usage : $value = $self->dbm_package();
$self->dbm_package($value);
- Function: Gets or sets the name of the Perl dbm module used.
+ Function: Gets or sets the name of the Perl dbm module used.
If the value is unset, then it returns the value of
the package variable $USE_DBM_TYPE or if that is
unset, then it chooses the best available dbm type,
- choosing 'DB_File' in preference to 'SDBM_File'.
+ choosing 'DB_File' in preference to 'SDBM_File'.
Bio::Abstract::Index may work with other dbm file
types.
@@ -329,10 +329,10 @@ sub default_id_parser
at the approprite place
This provides for a way to get the actual
- file contents and not an object
+ file contents and not an object
WARNING: you must parse the record deliminter
- *yourself*. Abstract wont do this for you
+ *yourself*. Abstract won't do this for you
So this code
$fh = $index->get_stream($myid);
@@ -349,7 +349,7 @@ sub default_id_parser
Returns : A filehandle object
Args : string represents the accession number
- Notes : This method should not be used without forethought
+ Notes : This method should not be used without forethought
=head2 open_dbm
@@ -359,7 +359,7 @@ sub default_id_parser
object. Write access is only given if explicitly
asked for by calling new(-write => 1) or having set
the write_flag(1) on the index object. The type of
- dbm file opened is that returned by dbm_package().
+ dbm file opened is that returned by dbm_package().
The name of the file to be is opened is obtained by
calling the filename() method.
@@ -375,8 +375,8 @@ sub default_id_parser
index module. Used to permanently identify an index
file as having been created by a particular version
of the index module. Must be provided by the sub class
- Example :
- Returns :
+ Example :
+ Returns :
Args : none
=head2 _filename
@@ -384,9 +384,9 @@ sub default_id_parser
Title : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=head2 _file_handle
@@ -409,7 +409,7 @@ sub default_id_parser
track the number of files indexed. Sets or gets
the number of files indexed when called with or
without an argument.
- Example :
+ Example :
Returns : INT
Args : INT
@@ -433,7 +433,7 @@ sub default_id_parser
Usage : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
joined by ASCII 034 (which is unlikely to be used
- in any of the strings), and returns it.
+ in any of the strings), and returns it.
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args : LIST
diff --git a/Bio/Index/Hmmer.pm b/Bio/Index/Hmmer.pm
index 0e6f735..8c48f94 100644
--- a/Bio/Index/Hmmer.pm
+++ b/Bio/Index/Hmmer.pm
@@ -1,12 +1,12 @@
#
# BioPerl module for Bio::Index::Hmmer
-#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+#
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Josh Lauricha <laurichj at bioinfo.ucr.edu>
#
# Copyright Josh Lauricha
-# Unless otherwise noted, this was shamelessly ripped from
+# Unless otherwise noted, this was shamelessly ripped from
# Bio::Index::Blast
#
# You may distribute this module under the terms of perl itself
@@ -57,7 +57,7 @@ This object allows one to build an index on a HMMER file (or files)
and provide quick access to the HMMER report for that accession.
For best results 'use strict'.
-You can also set or customize the unique key used to retrieve by
+You can also set or customize the unique key used to retrieve by
writing your own function and calling the id_parser() method.
For example:
@@ -84,15 +84,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -181,7 +181,7 @@ sub fetch_report
seek($fh, 0, 0); # The HMMER SearchIO wants the header, so we fetch it
while($line = <$fh>) {
- push @header, $line;
+ push @header, $line;
last if $line =~ /Query sequence:/o;
}
seek($fh, $pos, 0);
@@ -211,7 +211,7 @@ sub fetch_report
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
- parser for different flavours of blast dbs.
+ parser for different flavours of blast dbs.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
@@ -265,9 +265,9 @@ sub default_id_parser
Function: Specialist function to index HMMER report file(s).
Is provided with a filename and an integer
by make_index in its SUPER class.
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=cut
@@ -314,7 +314,7 @@ sub _index_file {
Usage : $value = $self->write_flag();
$self->write_flag($value);
Function: Gets or sets the value of write_flag, which
- is wether the dbm file should be opened with
+ is whether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
@@ -325,11 +325,11 @@ sub _index_file {
Usage : $value = $self->dbm_package();
$self->dbm_package($value);
- Function: Gets or sets the name of the Perl dbm module used.
+ Function: Gets or sets the name of the Perl dbm module used.
If the value is unset, then it returns the value of
the package variable $USE_DBM_TYPE or if that is
unset, then it chooses the best available dbm type,
- choosing 'DB_File' in preference to 'SDBM_File'.
+ choosing 'DB_File' in preference to 'SDBM_File'.
Bio::Abstract::Index may work with other dbm file
types.
@@ -346,10 +346,10 @@ sub _index_file {
at the approprite place
This provides for a way to get the actual
- file contents and not an object
+ file contents and not an object
WARNING: you must parse the record deliminter
- *yourself*. Abstract wont do this for you
+ *yourself*. Abstract won't do this for you
So this code
$fh = $index->get_stream($myid);
@@ -366,7 +366,7 @@ sub _index_file {
Returns : A filehandle object
Args : string represents the accession number
- Notes : This method should not be used without forethought
+ Notes : This method should not be used without forethought
=head2 open_dbm
@@ -376,7 +376,7 @@ sub _index_file {
object. Write access is only given if explicitly
asked for by calling new(-write => 1) or having set
the write_flag(1) on the index object. The type of
- dbm file opened is that returned by dbm_package().
+ dbm file opened is that returned by dbm_package().
The name of the file to be is opened is obtained by
calling the filename() method.
@@ -392,8 +392,8 @@ sub _index_file {
index module. Used to permanently identify an index
file as having been created by a particular version
of the index module. Must be provided by the sub class
- Example :
- Returns :
+ Example :
+ Returns :
Args : none
=head2 _filename
@@ -401,9 +401,9 @@ sub _index_file {
Title : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=head2 _file_handle
@@ -426,7 +426,7 @@ sub _index_file {
track the number of files indexed. Sets or gets
the number of files indexed when called with or
without an argument.
- Example :
+ Example :
Returns : INT
Args : INT
@@ -450,7 +450,7 @@ sub _index_file {
Usage : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
joined by ASCII 034 (which is unlikely to be used
- in any of the strings), and returns it.
+ in any of the strings), and returns it.
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args : LIST
diff --git a/Bio/Index/Stockholm.pm b/Bio/Index/Stockholm.pm
index 84e8328..a1fe668 100644
--- a/Bio/Index/Stockholm.pm
+++ b/Bio/Index/Stockholm.pm
@@ -13,7 +13,7 @@
=head1 NAME
-Bio::Index::Stockholm
+Bio::Index::Stockholm - Interface for indexing Stockholm files
=head1 SYNOPSIS
@@ -307,7 +307,7 @@ sub default_id_parser {
Usage : $value = $self->write_flag();
$self->write_flag($value);
Function: Gets or sets the value of write_flag, which
- is wether the dbm file should be opened with
+ is whether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
@@ -342,7 +342,7 @@ sub default_id_parser {
file contents and not an object
WARNING: you must parse the record deliminter
- *yourself*. Abstract wont do this for you
+ *yourself*. Abstract won't do this for you
So this code
$fh = $index->get_stream($myid);
diff --git a/Bio/LiveSeq/IO/Loader.pm b/Bio/LiveSeq/IO/Loader.pm
index ab2f4f6..417b733 100644
--- a/Bio/LiveSeq/IO/Loader.pm
+++ b/Bio/LiveSeq/IO/Loader.pm
@@ -135,7 +135,7 @@ sub entry2liveseq {
integer (optional) "flanking": amount of flanking bases to be kept
boolean (optional) "getswissprotinfo": if set to "0" it will avoid
trying to fetch information from a crossreference to a SwissProt
- entry, avoding the process of creation of AARange objects
+ entry, avoiding the process of creation of AARange objects
It is "1" (on) by default
Alternative to a gene_name, a position can be given: an
diff --git a/Bio/LiveSeq/IO/README b/Bio/LiveSeq/IO/README
index 923811a..4ca8ef1 100644
--- a/Bio/LiveSeq/IO/README
+++ b/Bio/LiveSeq/IO/README
@@ -14,7 +14,7 @@ Bio::LiveSeq::IO::Loader
Bio::LiveSeq::IO::BioPerl
- is the preferred method which uses Bio::DB::EMBL to retrive
+ is the preferred method which uses Bio::DB::EMBL to retrieve
sequences over the Web by accession number.
Bio::LiveSeq::IO::SRS
diff --git a/Bio/LiveSeq/Mutation.pm b/Bio/LiveSeq/Mutation.pm
index b5b91c4..823ae8c 100644
--- a/Bio/LiveSeq/Mutation.pm
+++ b/Bio/LiveSeq/Mutation.pm
@@ -17,7 +17,7 @@ Bio::LiveSeq::Mutation - Mutation event descriptor class
=head1 SYNOPSIS
- # full descrition of a point mutation
+ # full description of a point mutation
$mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
-seqori => 'T',
-pos => 100,
diff --git a/Bio/LiveSeq/SeqI.pm b/Bio/LiveSeq/SeqI.pm
index 0197f73..9536a96 100644
--- a/Bio/LiveSeq/SeqI.pm
+++ b/Bio/LiveSeq/SeqI.pm
@@ -248,7 +248,7 @@ sub labelsubseq {
length, integer, '' or undef
an optional strand (1 or -1) 4th argument
if strand argument is not given, it will default to the object
- argment. This argument is useful when a call is issued from a child
+ argument. This argument is useful when a call is issued from a child
of a parent object containing the subseq method
=cut
@@ -386,7 +386,7 @@ sub display_id {
Function: Returns the unique biological id for a sequence, commonly
called the accession_number.
Notice that primary_id() provides the unique id for the
- implemetation, allowing multiple objects to have the same accession
+ implementation, allowing multiple objects to have the same accession
number in a particular implementation.
For objects with no accession_number this method returns "unknown".
diff --git a/Bio/LocatableSeq.pm b/Bio/LocatableSeq.pm
index 2d15f9b..2fff649 100644
--- a/Bio/LocatableSeq.pm
+++ b/Bio/LocatableSeq.pm
@@ -655,7 +655,7 @@ sub trunc {
sub validate_seq {
my ($self, $seqstr, $throw) = @_;
$seqstr = '' if not defined $seqstr;
- $throw = 0 if not defined $throw ; # 0 for backward compatiblity
+ $throw = 0 if not defined $throw ; # 0 for backward compatibility
if ( (CORE::length $seqstr > 0 ) &&
($seqstr !~ /^([$MATCHPATTERN]+)$/) ) {
if ($throw) {
diff --git a/Bio/Location/Atomic.pm b/Bio/Location/Atomic.pm
index 205a317..54a1074 100644
--- a/Bio/Location/Atomic.pm
+++ b/Bio/Location/Atomic.pm
@@ -91,7 +91,7 @@ sub new {
# Do
# my $location = $f1->location->union($f2->location);
# We get an error without the following code which
- # explictly loads the Bio::Location::Simple class
+ # explicitly loads the Bio::Location::Simple class
unless( $class->can('start') ) {
eval { Bio::Root::Root->_load_module($class) };
if ( $@ ) {
@@ -132,7 +132,7 @@ sub new {
Usage : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
- Args : optionaly allows the start to be set
+ Args : optionally allows the start to be set
: using $loc->start($start)
=cut
@@ -149,7 +149,7 @@ sub start {
Usage : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
- Args : optionaly allows the end to be set
+ Args : optionally allows the end to be set
: using $loc->end($start)
=cut
@@ -167,7 +167,7 @@ sub end {
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandidness (-1, 0, +1)
- Args : optionaly allows the strand to be set
+ Args : optionally allows the strand to be set
: using $loc->strand($strand)
=cut
@@ -480,7 +480,7 @@ sub valid_Location {
The interface *does not* require implementing classes to
accept setting of a different policy. The implementation
- provided here does, however, allow to do so.
+ provided here does, however, allow one to do so.
Implementors of this interface are expected to initialize
every new instance with a
diff --git a/Bio/Location/Fuzzy.pm b/Bio/Location/Fuzzy.pm
index fa81669..49129dd 100644
--- a/Bio/Location/Fuzzy.pm
+++ b/Bio/Location/Fuzzy.pm
@@ -438,7 +438,7 @@ sub end_pos_type {
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
- does, however, allow to do so.
+ does, however, allow one to do so.
Implementors of this interface are expected to initialize every
new instance with a CoordinatePolicyI object. The implementation
diff --git a/Bio/Location/FuzzyLocationI.pm b/Bio/Location/FuzzyLocationI.pm
index 882279e..2db6e9f 100644
--- a/Bio/Location/FuzzyLocationI.pm
+++ b/Bio/Location/FuzzyLocationI.pm
@@ -182,7 +182,7 @@ Bio::LocationI methods follow
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
- does, however, allow to do so.
+ does, however, allow one to do so.
Implementors of this interface are expected to initialize every
new instance with a CoordinatePolicyI object. The implementation
diff --git a/Bio/Location/Simple.pm b/Bio/Location/Simple.pm
index 18edf60..c59c609 100644
--- a/Bio/Location/Simple.pm
+++ b/Bio/Location/Simple.pm
@@ -109,7 +109,7 @@ sub new {
Usage : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
- Args : optionaly allows the start to be set
+ Args : optionally allows the start to be set
using $loc->start($start)
=cut
@@ -134,7 +134,7 @@ sub start {
Usage : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
- Args : optionaly allows the end to be set
+ Args : optionally allows the end to be set
: using $loc->end($start)
Note : If start is set but end is undefined, this now assumes that start
is the same as end but throws a warning (i.e. it assumes this is
@@ -173,7 +173,7 @@ sub end {
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandedness (-1, 0, +1)
- Args : optionaly allows the strand to be set
+ Args : optionally allows the strand to be set
: using $loc->strand($strand)
=cut
diff --git a/Bio/Location/Split.pm b/Bio/Location/Split.pm
index 5ae46e9..dede2c4 100644
--- a/Bio/Location/Split.pm
+++ b/Bio/Location/Split.pm
@@ -798,7 +798,7 @@ sub seq_id {
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
- does, however, allow to do so.
+ does, however, allow one to do so.
Implementors of this interface are expected to initialize every
new instance with a CoordinatePolicyI object. The implementation
diff --git a/Bio/Location/SplitLocationI.pm b/Bio/Location/SplitLocationI.pm
index 1930392..41a45bc 100644
--- a/Bio/Location/SplitLocationI.pm
+++ b/Bio/Location/SplitLocationI.pm
@@ -223,7 +223,7 @@ Bio::LocationI inherited methods follow
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
- does, however, allow to do so.
+ does, however, allow one to do so.
Implementors of this interface are expected to initialize every
new instance with a CoordinatePolicyI object. The implementation
diff --git a/Bio/LocationI.pm b/Bio/LocationI.pm
index 48dedec..404e145 100644
--- a/Bio/LocationI.pm
+++ b/Bio/LocationI.pm
@@ -358,7 +358,7 @@ sub is_remote{
The interface *does not* require implementing classes to
accept setting of a different policy. The implementation
- provided here does, however, allow to do so.
+ provided here does, however, allow one to do so.
Implementors of this interface are expected to initialize
every new instance with a
diff --git a/Bio/Map/CytoMarker.pm b/Bio/Map/CytoMarker.pm
index 7466c30..814e4e9 100644
--- a/Bio/Map/CytoMarker.pm
+++ b/Bio/Map/CytoMarker.pm
@@ -22,7 +22,7 @@ Bio::Map::CytoMarker - An object representing a marker.
=head1 DESCRIPTION
-This object handles markers with a positon in a cytogenetic map known.
+This object handles markers with a position in a cytogenetic map known.
This marker will have a name and a position.
=head1 FEEDBACK
diff --git a/Bio/Map/CytoPosition.pm b/Bio/Map/CytoPosition.pm
index 82a8ab6..845ce5c 100644
--- a/Bio/Map/CytoPosition.pm
+++ b/Bio/Map/CytoPosition.pm
@@ -36,12 +36,12 @@ cytogenetic map. See L<Bio::Map::MarkerI> for more information.
Cytogenetic locations are names of bands visible in stained mitotic
eucaryotic chromosomes. The naming follows strict rules which are
-consistant at least in higher vertebates, e.g. mammals. The chromosome
+consistent at least in higher vertebates, e.g. mammals. The chromosome
name preceds the band names.
The shorter arm of the chromosome is called 'p' ('petit') and usually
drawn pointing up. The lower arm is called 'q' ('queue'). The bands
-are named from the region separting these, a centromere (cen), towards
+are named from the region separating these, a centromere (cen), towards
the tips or telomeric regions (ter) counting from 1 upwards. Depending
of the resolution used the bands are identified with one or more
digit. The first digit determines the major band and subsequent digits
@@ -517,7 +517,7 @@ sub range2value {
Title : value
Usage : my $pos = $position->value;
- Function: Get/Set the value for this postion
+ Function: Get/Set the value for this position
Returns : scalar, value
Args : none to get, OR scalar to set
diff --git a/Bio/Map/GeneRelative.pm b/Bio/Map/GeneRelative.pm
index 00d0859..2cab5a9 100755
--- a/Bio/Map/GeneRelative.pm
+++ b/Bio/Map/GeneRelative.pm
@@ -21,7 +21,7 @@ Bio::Map::GeneRelative - Represents being relative to named sub-regions of a
use Bio::Map::GeneRelative;
- # say that a somthing will have a position relative to the start of the
+ # say that a something will have a position relative to the start of the
# gene on map
my $rel = Bio::Map::GeneRelative->new(-gene => 0);
@@ -202,7 +202,7 @@ sub absolute_conversion {
return $self->SUPER::absolute_conversion($pos);
}
if (ref($value)) {
- # psuedo-recurse
+ # pseudo-recurse
my $rel = $value->relative;
$value = $rel->absolute_conversion($value);
}
diff --git a/Bio/Map/Microsatellite.pm b/Bio/Map/Microsatellite.pm
index db5949d..ea7eaa4 100644
--- a/Bio/Map/Microsatellite.pm
+++ b/Bio/Map/Microsatellite.pm
@@ -103,7 +103,7 @@ use base qw(Bio::Map::Marker);
default 'Unknown microsatellite')
-positions => position(s) for this marker in maps[optional],
An array reference of tuples (array refs themselves)
- Each tuple conatins a Bio::Map::MapI-inherited object and a
+ Each tuple contains a Bio::Map::MapI-inherited object and a
Bio::Map::PositionI-inherited obj, no default)
-sequence => the sequence of this microsatellite (optional,
scalar, no default)
diff --git a/Bio/Map/OrderedPosition.pm b/Bio/Map/OrderedPosition.pm
index c59a49b..1f54dd1 100644
--- a/Bio/Map/OrderedPosition.pm
+++ b/Bio/Map/OrderedPosition.pm
@@ -176,7 +176,7 @@ sub equals {
# admittedly these aren't really the best comparisons in the world
# but it is a first pass we'll need to refine the algorithm or not
-# provide general comparisions and require these to be implemented
+# provide general comparisons and require these to be implemented
# by objects closer to the specific type of data
=head2 less_than
diff --git a/Bio/Map/Physical.pm b/Bio/Map/Physical.pm
index d6429ac..2f5e4bd 100755
--- a/Bio/Map/Physical.pm
+++ b/Bio/Map/Physical.pm
@@ -19,7 +19,7 @@ Bio::Map::Physical - A class for handling a Physical Map (such as FPC)
use Bio::MapIO;
- # accquire a Bio::Map::Physical using Bio::MapIO::fpc
+ # acquire a Bio::Map::Physical using Bio::MapIO::fpc
my $mapio = Bio::MapIO->new(-format => "fpc",-file => "rice.fpc",
-readcor => 0);
diff --git a/Bio/Map/Position.pm b/Bio/Map/Position.pm
index 1a17e91..575ec5e 100644
--- a/Bio/Map/Position.pm
+++ b/Bio/Map/Position.pm
@@ -229,7 +229,7 @@ sub absolute {
Title : value
Usage : my $pos = $position->value;
- Function: Get/Set the value for this postion
+ Function: Get/Set the value for this position
Returns : scalar, value
Args : [optional] new value to set
diff --git a/Bio/Map/PositionI.pm b/Bio/Map/PositionI.pm
index 3ac3018..466683b 100644
--- a/Bio/Map/PositionI.pm
+++ b/Bio/Map/PositionI.pm
@@ -23,7 +23,7 @@ Bio::Map::PositionI - Abstracts the notion of a position having a value in the c
=head1 DESCRIPTION
-This object stores one of the postions that a mappable object
+This object stores one of the positions that a mappable object
(e.g. Marker) may have in a map.
Positions can have non-numeric values or other methods to store the locations,
diff --git a/Bio/Map/Relative.pm b/Bio/Map/Relative.pm
index bbe3dcb..bc24634 100755
--- a/Bio/Map/Relative.pm
+++ b/Bio/Map/Relative.pm
@@ -183,7 +183,7 @@ sub absolute_conversion {
$self->throw("Relative to a Mappable, but this Mappable has no positions on the supplied Position's map") unless $value;
}
if (ref($value)) {
- # psuedo-recurse
+ # pseudo-recurse
my $rel = $value->relative;
$value = $rel->absolute_conversion($value);
}
diff --git a/Bio/Map/TranscriptionFactor.pm b/Bio/Map/TranscriptionFactor.pm
index 9769aa0..384108b 100644
--- a/Bio/Map/TranscriptionFactor.pm
+++ b/Bio/Map/TranscriptionFactor.pm
@@ -48,7 +48,7 @@ element
=head1 DESCRIPTION
-A transcription factor modelled as a mappable element. It can have mulitple
+A transcription factor modelled as a mappable element. It can have multiple
binding sites (positions) near multiple genes (maps).
=head1 FEEDBACK
diff --git a/Bio/Matrix/Generic.pm b/Bio/Matrix/Generic.pm
index 9f4f061..4debd9e 100644
--- a/Bio/Matrix/Generic.pm
+++ b/Bio/Matrix/Generic.pm
@@ -198,13 +198,14 @@ sub matrix_name{
=head2 entry
Title : entry
- Usage : my $entry = $matrix->entry($row,$col)
+ Usage : my $entry = $matrix->entry($row,$col,$value)
Function: Get the value for a specific cell as specified
by the row and column names
Returns : scalar value or undef if row or col does not
exist
Args : $rowname - name of the row
$colname - column name
+ $value - [optional] New value for the entry
=cut
@@ -222,11 +223,12 @@ sub entry{
=head2 get_entry
Title : get_entry
- Usage : my $entry = $matrix->get_entry($rowname,$columname)
+ Usage : my $entry = $matrix->get_entry($rowname,$columname,$value)
Function: Get the entry for a given row,column pair
Returns : scalar
Args : $row name
$column name
+ $value
=cut
diff --git a/Bio/Matrix/PSM/IO.pm b/Bio/Matrix/PSM/IO.pm
index 9639ab3..d1b8dc9 100644
--- a/Bio/Matrix/PSM/IO.pm
+++ b/Bio/Matrix/PSM/IO.pm
@@ -147,7 +147,7 @@ sub new {
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
'scoring';
- $class->throw("$format format unrecognized or an argument error occured\n.") if (!grep(/$format/, at Bio::Matrix::PSM::IO::PSMFORMATS));
+ $class->throw("$format format unrecognized or an argument error occurred\n.") if (!grep(/$format/, at Bio::Matrix::PSM::IO::PSMFORMATS));
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
diff --git a/Bio/Matrix/PSM/IO/masta.pm b/Bio/Matrix/PSM/IO/masta.pm
index 0644c28..9f418f7 100755
--- a/Bio/Matrix/PSM/IO/masta.pm
+++ b/Bio/Matrix/PSM/IO/masta.pm
@@ -195,7 +195,7 @@ sub next_psm {
if ($line !~ /[^ACGTacgt]/g) {
# This is a set of aligned sequences
- $self->throw("Mixing between types is not allowed or a parsing error occured\n")
+ $self->throw("Mixing between types is not allowed or a parsing error occurred\n")
if (($self->{_mtype} != 3) && ($mtype)) ;
$self->throw("Bad sequence- different length: $line\n")
if (($len) && ($len!=length($line)));
@@ -209,12 +209,12 @@ sub next_psm {
$line=~s/[\s\t]+/\t/g;
my @data=split(/[\s\t]+/,$line);
if ($#data==3) {
- $self->throw("Mixing between types is not allowed or a parsing error occured\n") if (($mtype)&&($self->{_mtype} !=1)) ;
+ $self->throw("Mixing between types is not allowed or a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=1)) ;
$self->{_mtype}=1;
$mtype=1;
}
else {
- $self->throw("Mixing between types is not allowedor a parsing error occured\n") if (($mtype)&&($self->{_mtype} !=2)) ;
+ $self->throw("Mixing between types is not allowedor a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=2)) ;
$self->{_mtype}=2;
$mtype=1;
}
diff --git a/Bio/Matrix/PSM/InstanceSite.pm b/Bio/Matrix/PSM/InstanceSite.pm
index 123cb11..9b6318d 100644
--- a/Bio/Matrix/PSM/InstanceSite.pm
+++ b/Bio/Matrix/PSM/InstanceSite.pm
@@ -1,7 +1,7 @@
=head1 NAME
-Bio::Matrix::PSM::InstanceSite - A PSM site occurance
+Bio::Matrix::PSM::InstanceSite - A PSM site occurrence
=head1 SYNOPSIS
diff --git a/Bio/Matrix/PSM/ProtMatrix.pm b/Bio/Matrix/PSM/ProtMatrix.pm
index 337d76c..2bd5eab 100644
--- a/Bio/Matrix/PSM/ProtMatrix.pm
+++ b/Bio/Matrix/PSM/ProtMatrix.pm
@@ -109,7 +109,7 @@ example A matrix is given as array, C - as string). The position
vector is (0,0,0,0). One of the probability vectors is shorter than
the rest.
-Summary of the methods I use most frequently (details bellow):
+Summary of the methods I use most frequently (details below):
iupac - return IUPAC compliant consensus as a string
score - Returns the score as a real number
@@ -316,7 +316,7 @@ sub _calculate_consensus {
Title : next_pos
Usage :
- Function : Retrives the next position features: frequencies for all 20 amino
+ Function : Retrieves the next position features: frequencies for all 20 amino
acids, log-odds scores for all 20 amino acids at this position,
the main (consensus) letter at this position, the probability
for the consensus letter to occur at this position and the relative
@@ -720,7 +720,7 @@ sub _uncompress_string {
Usage :
Function: A method to provide a compressed frequency vector. It uses one byte to
code the frequence for one of the probability vectors for one position.
- Useful for relational database. Improvment of the previous 0..a coding.
+ Useful for relational database. Improvement of the previous 0..a coding.
Throws :
Example : my $strA=$self->get_compressed_freq('A');
Returns : String
diff --git a/Bio/Matrix/PSM/ProtPsm.pm b/Bio/Matrix/PSM/ProtPsm.pm
index cfadbe7..6c3268f 100644
--- a/Bio/Matrix/PSM/ProtPsm.pm
+++ b/Bio/Matrix/PSM/ProtPsm.pm
@@ -53,7 +53,7 @@ mast, meme, transfac, theiresias, etc.? To me the best way is to return
SiteMatrix object + arrray of InstanceSite objects and then mast will return
undef for SiteMatrix and transfac will return undef for InstanceSite. Probably
I cannot see some other design issues that might arise from such approach, but
-it seems more straightforward. Hilmar does not like this beacause it is an
+it seems more straightforward. Hilmar does not like this because it is an
exception from the general BioPerl rules. Should I leave this as an option?
Also the header rightfully belongs the driver object, and could be retrieved as
hashes. I do not think it can be done any other way, unless we want to create
diff --git a/Bio/Matrix/PSM/Psm.pm b/Bio/Matrix/PSM/Psm.pm
index fe53823..1a427da 100644
--- a/Bio/Matrix/PSM/Psm.pm
+++ b/Bio/Matrix/PSM/Psm.pm
@@ -41,7 +41,7 @@ Bio::Matrix::PSM::Psm - handle combination of site matricies
# where pA through pG are the respective frequencies of the matrix (see also
# Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory,
# except for -instances (reference to an array of
- # Bio::Matrix::PSM::InstanceSite objects) which is documented bellow.
+ # Bio::Matrix::PSM::InstanceSite objects) which is documented below.
=head1 DESCRIPTION
@@ -67,7 +67,7 @@ arrray of InstanceSite objects and then mast will return undef for
SiteMatrix and transfac will return undef for InstanceSite. Probably I
cannot see some other design issues that might arise from such
approach, but it seems more straightforward. Hilmar does not like
-this beacause it is an exception from the general BioPerl rules Should
+this because it is an exception from the general BioPerl rules Should
I leave this as an option? Also the header rightfully belongs the
driver object, and could be retrieved as hashes. I do not think it
can be done any other way, unless we want to create even one more
diff --git a/Bio/Matrix/PSM/PsmI.pm b/Bio/Matrix/PSM/PsmI.pm
index 9ced3f0..b3f64c1 100644
--- a/Bio/Matrix/PSM/PsmI.pm
+++ b/Bio/Matrix/PSM/PsmI.pm
@@ -41,7 +41,7 @@ Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
# Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory,
# except for
#-instances (reference to an array of Bio::Matrix::PSM::InstanceSite objects)
- # which is documented bellow.
+ # which is documented below.
=head1 DESCRIPTION
@@ -66,7 +66,7 @@ way is to return SiteMatrix object + arrray of InstanceSite objects
and then mast will return undef for SiteMatrix and transfac will
return undef for InstanceSite. Probably I cannot see some other design
issues that might arise from such approach, but it seems more
-straightforward. Hilmar does not like this beacause it is an
+straightforward. Hilmar does not like this because it is an
exception from the general BioPerl rules Should I leave this as an
option? Also the header rightfully belongs the driver object, and
could be retrieved as hashes. I do not think it can be done any other
diff --git a/Bio/Matrix/PSM/SiteMatrix.pm b/Bio/Matrix/PSM/SiteMatrix.pm
index 4e12b20..85b026c 100644
--- a/Bio/Matrix/PSM/SiteMatrix.pm
+++ b/Bio/Matrix/PSM/SiteMatrix.pm
@@ -17,7 +17,7 @@ position scoring matrix (or position weight matrix) and log-odds
#or
my ($a,$c,$g,$t,$score,$ic,$mid)=('05a011','110550','400001',
'100104',0.001,19.2,'CRE1');
- #Where a stands for all (this frequency=1), see explanation bellow
+ #Where a stands for all (this frequency=1), see explanation below
my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,
-lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l,
-IC=>$ic,-e_val=>$score, -id=>$mid);
@@ -75,7 +75,7 @@ Throws an exception if: You mix as an input array and string (for example A
matrix is given as array, C - as string). The position vector is (0,0,0,0). One
of the probability vectors is shorter than the rest.
-Summary of the methods I use most frequently (details bellow):
+Summary of the methods I use most frequently (details below):
iupac - return IUPAC compliant consensus as a string
score - Returns the score as a real number
@@ -188,7 +188,7 @@ use base qw(Bio::Root::Root Bio::Matrix::PSM::SiteMatrixI);
-sites => int, the number of sites that went into this matrix
-model => hash ref, background frequencies for A, C, G and T
-correction => number, the number to add to all positions to achieve
- psuedo count correction (default 0: no correction)
+ pseudo count correction (default 0: no correction)
NB: do not use correction when your input is
frequences!
-accession_number => string, an accession number
@@ -273,7 +273,7 @@ sub new {
$self->throw("Position meaningless-all frequencies are 0");
}
- # apply psuedo-count correction to all values - this will result in
+ # apply pseudo-count correction to all values - this will result in
# very bad frequencies if the input is already frequences and a
# correction value as large as 1 is used!
if ($self->{correction}) {
@@ -360,7 +360,7 @@ sub calc_weight {
Title : next_pos
Usage :
- Function: Retrives the next position features: frequencies for A,C,G,T, the
+ Function: Retrieves the next position features: frequencies for A,C,G,T, the
main letter (as in consensus) and the probabilty for this letter to
occur at this position and the current position
Returns : hash (pA,pC,pG,pT,logA,logC,logG,logT,base,prob,rel)
@@ -877,7 +877,7 @@ sub _uncompress_string {
Usage :
Function: A method to provide a compressed frequency vector. It uses one byte
to code the frequence for one of the probability vectors for one
- position. Useful for relational database. Improvment of the previous
+ position. Useful for relational database. Improvement of the previous
0..a coding.
Example : my $strA=$self->get_compressed_freq('A');
Returns : String
diff --git a/Bio/Matrix/PSM/SiteMatrixI.pm b/Bio/Matrix/PSM/SiteMatrixI.pm
index 1bcff3b..a41365e 100644
--- a/Bio/Matrix/PSM/SiteMatrixI.pm
+++ b/Bio/Matrix/PSM/SiteMatrixI.pm
@@ -30,7 +30,7 @@ Throws an exception if: You mix as an input array and string (for example A
matrix is given as array, C - as string). The position vector is (0,0,0,0). One
of the probability vectors is shorter than the rest.
-Summary of the methods I use most frequently (details bellow):
+Summary of the methods I use most frequently (details below):
iupac - return IUPAC compliant consensus as a string
score - Returns the score as a real number
@@ -469,7 +469,7 @@ sub _uncompress_string {
Usage :
Function: A method to provide a compressed frequency vector. It uses one byte to
code the frequence for one of the probability vectors for one position.
- Useful for relational database. Improvment of the previous 0..a coding.
+ Useful for relational database. Improvement of the previous 0..a coding.
Throws :
Example : my $strA=$self->get_compressed_freq('A');
Returns : String
diff --git a/Bio/Ontology/OntologyStore.pm b/Bio/Ontology/OntologyStore.pm
index af96765..4ebd524 100644
--- a/Bio/Ontology/OntologyStore.pm
+++ b/Bio/Ontology/OntologyStore.pm
@@ -28,7 +28,7 @@ Bio::Ontology::OntologyStore - A repository of ontologies
my $cell_ontology = $io->next_ontology;
#this is a singleton that caches the fact that you've created
- #a 'Cell Ontology' intance...
+ #a 'Cell Ontology' instance...
my $store = Bio::Ontology::OntologyStore->get_instance();
#...and it can hand you back a copy of it at any time.
diff --git a/Bio/Ontology/SimpleOntologyEngine.pm b/Bio/Ontology/SimpleOntologyEngine.pm
index 7abf54e..c4ba99c 100644
--- a/Bio/Ontology/SimpleOntologyEngine.pm
+++ b/Bio/Ontology/SimpleOntologyEngine.pm
@@ -535,7 +535,7 @@ sub get_all_relationships {
Title : get_predicate_terms
Usage : get_predicate_terms(): TermI
- Function: Retrives all relationship types stored in the engine
+ Function: Retrieves all relationship types stored in the engine
Example :
Returns : reference to an array of Bio::Ontology::RelationshipType objects
Args :
diff --git a/Bio/Ontology/Term.pm b/Bio/Ontology/Term.pm
index dfd1060..21f5136 100644
--- a/Bio/Ontology/Term.pm
+++ b/Bio/Ontology/Term.pm
@@ -164,7 +164,7 @@ sub new {
defined($is_obsolete) && $self->is_obsolete( $is_obsolete );
defined($comment) && $self->comment( $comment );
defined($dbxrefs) && $self->add_dbxref(-dbxrefs => $dbxrefs);
- # deprecated methods, allow to pass on to get the dep. notification
+ # deprecated methods, allow one to pass on to get the dep. notification
ref($dblinks) && $self->add_dblink(@$dblinks);
ref($references) && $self->add_reference(@$references);
@@ -938,7 +938,7 @@ sub description {
=head1 Deprecated methods
-Used for looking up the methods that supercedes them.
+Used for looking up the methods that supersedes them.
=cut
diff --git a/Bio/Ontology/TermI.pm b/Bio/Ontology/TermI.pm
index bf90012..cc5338a 100644
--- a/Bio/Ontology/TermI.pm
+++ b/Bio/Ontology/TermI.pm
@@ -340,7 +340,7 @@ sub get_secondary_ids {
=head1 Deprecated methods
-Used for looking up the methods that supercedes them.
+Used for looking up the methods that supersedes them.
=cut
diff --git a/Bio/OntologyIO/Handlers/BaseSAXHandler.pm b/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
index 5a10f90..dffd9d8 100644
--- a/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
+++ b/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
@@ -1,11 +1,11 @@
#
# BioPerl module for BaseSAXHandler
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Juguang Xiao, juguang at tll.org.sg
#
-# Copyright Juguang Xiao
+# Copyright Juguang Xiao
#
# You may distribute this module under the same terms as perl itself
@@ -13,7 +13,7 @@
=head1 NAME
-Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers
+Bio::OntologyIO::Handlers::BaseSAXHandler - base class for SAX Handlers
=head1 SYNOPSIS
@@ -21,8 +21,8 @@ See description.
=head1 DESCRIPTION
-This module is an abstract module, serving as the base of any SAX Handler
-implementation. It tries to offer the framework that SAX handlers generally
+This module is an abstract module, serving as the base of any SAX Handler
+implementation. It tries to offer the framework that SAX handlers generally
need, such as tag_stack, char_store, etc.
In the implementation handler, you can take advantage of this based module by
@@ -80,15 +80,15 @@ Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -106,7 +106,7 @@ Juguang Xiao, juguang at tll.org.sg
=head2 APPENDIX
The rest of the documentation details each of the object methods.
-Interal methods are usually preceded with a _
+Internal methods are usually preceded with a _
=cut
@@ -135,8 +135,8 @@ sub _initialize {
Title : _tag_stack
Usage : @tags = $self->_tag_stack;
Function: Get an array of tags that have been accessed but not enclosed.
- Return :
- Args :
+ Return :
+ Args :
=cut
@@ -168,7 +168,7 @@ sub _pop_tag {
Usage : $top = $self->_top_tag;
Function: get the top tag in the tag stack.
Return : a tag name
- Args : [none]
+ Args : [none]
=cut
diff --git a/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm b/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
index 0f74fdb..8908ba8 100644
--- a/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
+++ b/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
@@ -58,7 +58,7 @@ Hilmar Lapp, hlapp at gmx.net
=head2 APPENDIX
The rest of the documentation details each of the object methods.
-Interal methods are usually preceded with a _
+Internal methods are usually preceded with a _
=cut
@@ -323,7 +323,7 @@ sub _persist_relationship {
relationship types.
Example :
- Returns : the ontology as a peristent object with primary key
+ Returns : the ontology as a persistent object with primary key
Args : the ontology to persist as a Bio::Ontology::OntologyI
compliant object
diff --git a/Bio/OntologyIO/obo.pm b/Bio/OntologyIO/obo.pm
index 662a635..6f44285 100644
--- a/Bio/OntologyIO/obo.pm
+++ b/Bio/OntologyIO/obo.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::OntologyIO::obo
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Sohel Merchant, s-merchant at northwestern.edu
#
@@ -12,7 +12,7 @@
=head1 NAME
-Bio::OntologyIO::obo
+Bio::OntologyIO::obo - parser for OBO flat-file format
=head1 SYNOPSIS
@@ -63,15 +63,15 @@ Bioperl mailing lists Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -465,7 +465,7 @@ sub _ont_engine {
$self->{"_ont_engine"};
}
-# Removes the escape chracters from the file
+# Removes the escape characters from the file
sub _filter_line {
my ( $self, $line ) = @_;
@@ -505,7 +505,7 @@ sub _header {
if ( !$line ) {
if ( !$format_version_header_flag ) {
- $self->throw("Format Error - Cannot find tag format-version." .
+ $self->throw("Format Error - Cannot find tag format-version." .
"This is required in header" );
}
@@ -515,7 +515,7 @@ sub _header {
# Check if there is a header
if ( $line =~ /\[\w*\]/ ) {
- $self->throw("Format Error - Cannot find tag format-version." .
+ $self->throw("Format Error - Cannot find tag format-version." .
"This is required in header." );
}
@@ -533,7 +533,7 @@ sub _header {
|default-namespace:
|remark:
|subsetdef:
- |import:
+ |import:
|synonymtypedef:
|idspace:
|default-relationship-id-prefix:
@@ -792,7 +792,7 @@ sub _split_on_comma {
sub _check_colon {
my ( $self, $line, $line_no ) = @_;
if ( $line && !( $line =~ /:/ ) ) {
- $self->throw("OBO File Format Error on line $line_no $line\n" .
+ $self->throw("OBO File Format Error on line $line_no $line\n" .
"Cannot find key-terminating colon"
);
}
diff --git a/Bio/ParameterBaseI.pm b/Bio/ParameterBaseI.pm
index 44f4d9a..1c3bbe7 100644
--- a/Bio/ParameterBaseI.pm
+++ b/Bio/ParameterBaseI.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::ParameterBaseI
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
@@ -87,7 +87,7 @@ Implementing classes use the following ways to set parameters:
2) Pass the parameters as a hash or array to set_parameters(), which sets the
parameters listed in the hash but leaves all others as is.
- $pobj->set_parameters(-retmax => 100, -retstart => 20);
+ $pobj->set_parameters(-retmax => 100, -retstart => 20);
3) Pass the parameters as a hash or array to reset_parameters(), which sets the
parameters listed in the hash and resets everything else.
@@ -107,18 +107,18 @@ ParameterBaseI object so that any object with a Bio::ParameterBaseI can decide
whether to submit a new request or return cached data. State changes are
revealed by the returned values of the parameters_changed() method, which is a
simple boolean set to TRUE when the object is first instantiated or parameters
-have changed.
+have changed.
When retrieving anything using the implementation-specific to_* methods (such as
to_query, to_string, to_uri, to_request, etc), the ParameterBaseI object state
is set to FALSE to indicate the data has been accessed and indicate reaccessing
will retrieve the same value. The observing object can then independently decide
-whether to rerun the cached query or return a previously cached result.
+whether to rerun the cached query or return a previously cached result.
One can also use indiviual getter/setters to retrieve single parameter values as
well as use parameter_hash() to retrieve all of the parameters in one go as a
hash. To check which parameters are available use available_parameters(). Args
-passed to
+passed to
=head1 FEEDBACK
@@ -131,17 +131,17 @@ of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l at lists.open-bio.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -178,7 +178,7 @@ use base qw(Bio::Root::RootI);
Usage : $pobj->set_parameters(%params);
Function: sets the parameters listed in the hash or array
Returns : None
- Args : [optional] hash or array of parameter/values.
+ Args : [optional] hash or array of parameter/values.
=cut
diff --git a/Bio/Perl.pm b/Bio/Perl.pm
index e619dc4..c6826b0 100644
--- a/Bio/Perl.pm
+++ b/Bio/Perl.pm
@@ -58,7 +58,7 @@ Bio::Perl - Functional access to BioPerl for people who don't know objects
$seq_object = get_sequence('genbank',"AI129902");
- # BLAST a sequence (assummes an internet connection)
+ # BLAST a sequence (assumes an internet connection)
$blast_report = blast_sequence($seq_object);
diff --git a/Bio/PopGen/HtSNP.pm b/Bio/PopGen/HtSNP.pm
index 17241c1..11da813 100644
--- a/Bio/PopGen/HtSNP.pm
+++ b/Bio/PopGen/HtSNP.pm
@@ -1133,7 +1133,7 @@ sub _remove_deg {
Title : _rem_silent_snp
Usage : _rem_silent_snp()
- Function: there is the remote possibilty that one SNP won't be a
+ Function: there is the remote possibility that one SNP won't be a
real SNP on this situation we have to remove this SNP,
otherwise the program won't find any tag
Returns : nonthing
@@ -1174,7 +1174,7 @@ sub _rem_silent_snp {
Usage :
Function: list of snps that are not SNPs. All values for that
SNPs on the set is the same one. Look stupid but can
- happend and if this happend you will not find any tag
+ happened and if this happend you will not find any tag
Returns : nothing
Args :
Status :
@@ -1442,7 +1442,7 @@ sub compare_arrays {
Title : _convert_to_numbers
Usage : _convert_to_numbers()
- Function: tranform the haplotype into numbers. before to do that
+ Function: transform the haplotype into numbers. before to do that
we have to consider the variation on the set.
Returns : nonthing
Args : ref to an AoA and a ref to an array
diff --git a/Bio/PopGen/Individual.pm b/Bio/PopGen/Individual.pm
index 66c5532..17632a4 100644
--- a/Bio/PopGen/Individual.pm
+++ b/Bio/PopGen/Individual.pm
@@ -113,7 +113,7 @@ sub new {
if( ref($genotypes) =~ /array/i ) {
$self->add_Genotype(@$genotypes);
} else {
- $self->warn("Must provide a valid array reference to set the genotypes value in the contructor");
+ $self->warn("Must provide a valid array reference to set the genotypes value in the constructor");
}
}
return $self;
diff --git a/Bio/PopGen/Population.pm b/Bio/PopGen/Population.pm
index 9149802..b14989b 100644
--- a/Bio/PopGen/Population.pm
+++ b/Bio/PopGen/Population.pm
@@ -244,7 +244,7 @@ sub set_Allele_Frequency {
FREQUENCY
FREQUENCIES
)], @args);
- if( defined $frequencies ) { # this supercedes the res
+ if( defined $frequencies ) { # this supersedes the res
if( ref($frequencies) =~ /HASH/i ) {
my ($markername,$alleles);
while( ($markername,$alleles) = each %$frequencies ) {
@@ -488,7 +488,7 @@ sub get_number_individuals{
Function: Fixes the number of individuals, call this with
0 to unset.
Only use this if you know what you are doing,
- this is only relavent when you are just adding
+ this is only relevant when you are just adding
allele frequency data for a population and want to
calculate something like theta
Returns : none
diff --git a/Bio/PopGen/TagHaplotype.pm b/Bio/PopGen/TagHaplotype.pm
index 7d37c5d..e8f036e 100644
--- a/Bio/PopGen/TagHaplotype.pm
+++ b/Bio/PopGen/TagHaplotype.pm
@@ -173,7 +173,7 @@ sub haplotype_block{
Title : input_block
Usage : $obj->input_block()
Function: returns haplotype block. By now will produce the same output than
- $self->haplotype_block. but for compatiblity, this method is kept.
+ $self->haplotype_block. but for compatibility, this method is kept.
This method is deprecated.
Returns : reference to array of array with the haplotype input value
Args : none
@@ -367,7 +367,7 @@ sub _generateCombinations{
Usage : internal
Function: take the haplotype and a list of possible combination
for that length. Generate a subset and scan it to find if
- the information is enought to define the haplotype set.
+ the information is enough to define the haplotype set.
Returns :
Args : none
Status : private
diff --git a/Bio/PrimarySeq.pm b/Bio/PrimarySeq.pm
index adffede..3ac172c 100644
--- a/Bio/PrimarySeq.pm
+++ b/Bio/PrimarySeq.pm
@@ -546,7 +546,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
- unique id for the implemetation, allowing multiple objects
+ unique id for the implementation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should
@@ -579,7 +579,7 @@ sub accession_number {
Usage : $unique_key = $seqobj->primary_id;
Function: Returns the unique id for this object in this
implementation. This allows implementations to manage their
- own object ids in a way the implementaiton can control
+ own object ids in a way the implementation can control
clients can expect one id to map to one object.
For sequences with no natural primary id, this method
@@ -801,7 +801,7 @@ This comprises of display_name and description.
Usage : $string = $seqobj->display_name();
Function: Get or set a string which is what should be displayed to the user.
The string should have no spaces (ideally, though a cautious
- user of this interface would not assumme this) and should be
+ user of this interface would not assume this) and should be
less than thirty characters (though again, double checking
this is a good idea).
@@ -852,8 +852,8 @@ actually implemented on Bio::PrimarySeqI
sequences this throws an exception of
"Sequence is a protein. Cannot revcom".
- The id is the same id as the orginal sequence, and the
- accession number is also indentical. If someone wants to
+ The id is the same id as the original sequence, and the
+ accession number is also identical. If someone wants to
track that this sequence has be reversed, it needs to
define its own extensions.
diff --git a/Bio/PrimarySeqI.pm b/Bio/PrimarySeqI.pm
index d699134..8e58370 100644
--- a/Bio/PrimarySeqI.pm
+++ b/Bio/PrimarySeqI.pm
@@ -53,7 +53,7 @@ Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
This object defines an abstract interface to basic sequence
information - for most users of the package the documentation (and
methods) in this class are not useful - this is a developers-only
-class which defines what methods have to be implmented by other Perl
+class which defines what methods have to be implemented by other Perl
objects to comply to the Bio::PrimarySeqI interface. Go "perldoc
Bio::Seq" or "man Bio::Seq" for more information on the main class for
sequences.
@@ -213,7 +213,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
- unique id for the implemetation, allowing multiple objects
+ unique id for the implementation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
@@ -236,7 +236,7 @@ sub accession_number {
Usage : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
implementation. This allows implementations to manage their
- own object ids in a way the implementaiton can control
+ own object ids in a way the implementation can control
clients can expect one id to map to one object.
For sequences with no accession number, this method should
@@ -347,7 +347,7 @@ are encouraged to override these methods
protein. Cannot revcom".
The id is the same id as the original sequence, and the
- accession number is also indentical. If someone wants to
+ accession number is also identical. If someone wants to
track that this sequence has be reversed, it needs to
define its own extensions.
diff --git a/Bio/PullParserI.pm b/Bio/PullParserI.pm
index a22d251..08f3121 100644
--- a/Bio/PullParserI.pm
+++ b/Bio/PullParserI.pm
@@ -47,7 +47,7 @@ would need to cache some data or otherwise behave differently during a
sequential read.
The main method in the system is get_field(). This method relies on the
-existance of a private hash reference accessible to it with the method
+existence of a private hash reference accessible to it with the method
_fields(). That hash ref should have as keys all the sorts of data you will want
to parse (eg. 'score'), and prior to parsing the values would be undefined. A
user of your module can then call either $module-E<gt>get_field('score') or
diff --git a/Bio/Restriction/Analysis.pm b/Bio/Restriction/Analysis.pm
index 436b2b5..1423f72 100644
--- a/Bio/Restriction/Analysis.pm
+++ b/Bio/Restriction/Analysis.pm
@@ -383,7 +383,7 @@ sub cut {
return $self;
}
-=head2 mulitple_digest
+=head2 multiple_digest
Title : multiple_digest
Function : perform a multiple digest on a sequence
diff --git a/Bio/Restriction/Enzyme.pm b/Bio/Restriction/Enzyme.pm
index 7a18baf..c72bfa2 100644
--- a/Bio/Restriction/Enzyme.pm
+++ b/Bio/Restriction/Enzyme.pm
@@ -646,7 +646,7 @@ sub revcom_site {
Note that the common notation ACCTGC(4/8) means that the forward
strand cut is four nucleotides after the END of the recognition
-site. The forwad cut in the coordinates used here in Acc36I
+site. The forward cut in the coordinates used here in Acc36I
ACCTGC(4/8) is at 6+4 i.e. 10.
Note that REBASE uses notation where cuts within symmetic sites are
diff --git a/Bio/Restriction/EnzymeI.pm b/Bio/Restriction/EnzymeI.pm
index b1eb36f..1136d6e 100644
--- a/Bio/Restriction/EnzymeI.pm
+++ b/Bio/Restriction/EnzymeI.pm
@@ -173,7 +173,7 @@ sub cuts_after { shift->throw_not_implemented; }
Note that the common notation ACCTGC(4/8) means that the forward
strand cut is four nucleotides after the END of the recognition
-site. The forwad cut in the coordinates used here in Acc36I
+site. The forward cut in the coordinates used here in Acc36I
ACCTGC(4/8) is at 6+4 i.e. 10.
Note that REBASE uses notation where cuts within symmetic sites are
diff --git a/Bio/Restriction/IO/base.pm b/Bio/Restriction/IO/base.pm
index 5942deb..ea3fbc7 100644
--- a/Bio/Restriction/IO/base.pm
+++ b/Bio/Restriction/IO/base.pm
@@ -267,8 +267,8 @@ sub _cuts_from_site {
Title : _meth
Usage : ($pos, $meth) = $self->_meth('2(5)');
- Function: Separates methylation postion and coce from a string.
- Adjusts the postion depending on enzyme site length
+ Function: Separates methylation position and coce from a string.
+ Adjusts the position depending on enzyme site length
and symmetry
Returns : array of position and methylation code
Args : 1. reference to Enzyme object
@@ -402,7 +402,7 @@ sub _make_multisites {
The examples we have of multiply cutting enzymes cut only four
times. This protected method deals only with a string of two
-integers separated with a slash, e.g. '12/7'. The numbers represent the postions
+integers separated with a slash, e.g. '12/7'. The numbers represent the positions
BEFORE the start of the recognition site, i.e. negative positions.
=cut
diff --git a/Bio/Restriction/IO/itype2.pm b/Bio/Restriction/IO/itype2.pm
index cb018eb..748ecf1 100644
--- a/Bio/Restriction/IO/itype2.pm
+++ b/Bio/Restriction/IO/itype2.pm
@@ -116,7 +116,7 @@ sub read {
chomp $line;
my ($name, $prototype, $site, $meth, $vendor, $refs) = split /\t/, $line;
- # we need mininum name and site
+ # we need minimum name and site
unless ($site) {
$self->warn("Can not parse line with name [$name]") if $self->verbose > 0;
next;
diff --git a/Bio/Root/Exception.pm b/Bio/Root/Exception.pm
index f2458b1..75aa0ef 100644
--- a/Bio/Root/Exception.pm
+++ b/Bio/Root/Exception.pm
@@ -119,7 +119,7 @@ Error.pm is not available.
=head2 Throwing exceptions within Bioperl modules
-Error.pm is not part of the Bioperl distibution, and may not be
+Error.pm is not part of the Bioperl distribution, and may not be
present within any given perl installation. So, when you want to
throw an exception in a Bioperl module, the safe way to throw it
is to use L<Bio::Root::Root/throw> which can use Error.pm
diff --git a/Bio/Root/Root.pm b/Bio/Root/Root.pm
index f8c9f2d..ce1a100 100644
--- a/Bio/Root/Root.pm
+++ b/Bio/Root/Root.pm
@@ -64,7 +64,7 @@ if it has also been installed.
If L<Error> has been installed, L<throw>() will use it. This causes an
Error.pm-derived object to be thrown. This can be caught within a
-C<catch{}> block, from wich you can extract useful bits of
+C<catch{}> block, from which you can extract useful bits of
information. If L<Error> is not installed, it will use the
L<Bio::Root::RootI>-based exception throwing facilty.
diff --git a/Bio/Root/Storable.pm b/Bio/Root/Storable.pm
index bf11df8..6dbc3d6 100644
--- a/Bio/Root/Storable.pm
+++ b/Bio/Root/Storable.pm
@@ -26,7 +26,7 @@ should be called during object instantiation.
Object storage is recursive; If the object being stored contains other
storable objects, these will be stored separately, and replaced by a
-skeleton object in the parent heirarchy. When the parent is later
+skeleton object in the parent hierarchy. When the parent is later
retrieved, its children remain in the skeleton state until explicitly
retrieved by the parent. This lazy-retrieve approach has obvious
memory efficiency benefits for certain applications.
@@ -106,7 +106,7 @@ sub _initialise_storable {
Arg [1] : string (optional)
Function : Accessor for the file to write state into.
- Should not normaly use as a setter - let Root::IO
+ Should not normally use as a setter - let Root::IO
do this for you.
Returntype: string
Exceptions:
diff --git a/Bio/Root/Test.pm b/Bio/Root/Test.pm
index 9c00068..62ee3c8 100644
--- a/Bio/Root/Test.pm
+++ b/Bio/Root/Test.pm
@@ -189,7 +189,7 @@ our @TEMP_FILES;
be skipped if either network tests
haven't been enabled in Build.PL or an
email hasn't been entered)
- -excludes_os => str (default none, if OS suppied, all tests
+ -excludes_os => str (default none, if OS supplied, all tests
will skip if running on that OS (eg.
'mswin'))
-framework => str (default 'Test::Most', the Test module
@@ -257,7 +257,7 @@ sub test_begin {
presence of a binary, skips if absent)
-requires_env => str (checks %ENV for a specific env. variable,
skips if absent)
- -excludes_os => str (default none, if OS suppied, desired num
+ -excludes_os => str (default none, if OS supplied, desired num
of tests will skip if running on that OS
(eg. 'mswin'))
-requires_networking => 1 (if true the desired number of tests will
@@ -484,7 +484,7 @@ sub _skip {
"unknown argument '$key' supplied, did you mistake 'required...' for 'requires...'?\n";
}
- # test user requirments and return
+ # test user requirements and return
if ($os) {
if ( $^O =~ /$os/i ) {
return ( 'Not compatible with your Operating System',
diff --git a/Bio/Root/Utilities.pm b/Bio/Root/Utilities.pm
index cf7eb6c..86bd720 100644
--- a/Bio/Root/Utilities.pm
+++ b/Bio/Root/Utilities.pm
@@ -125,7 +125,7 @@ $Util = Bio::Root::Root->new();
Title : date_format
Usage : $Util->date_format( [FMT], [DATE])
- Purpose : -- Get a string containing the formated date or time
+ Purpose : -- Get a string containing the formatted date or time
: taken when this routine is invoked.
: -- Provides a way to avoid using `date`.
: -- Provides an interface to localtime().
@@ -331,7 +331,7 @@ sub num2month {
: gzip, which is the default)
: -OUTFILE => String (name of the output compressed file, full path).
: -EXE => Name of executable for compression utility to use.
- : Will supercede those in @COMPRESSION_UTILS defined by
+ : Will supersede those in @COMPRESSION_UTILS defined by
: this module. If the absolute path to the executable is not provided,
: it will be searched in the PATH env variable.
Throws : Exception if file cannot be compressed.
@@ -455,7 +455,7 @@ sub compress {
: gzip, which is the default)
: -OUTFILE => String (name of the output uncompressed file, full path).
: -EXE => Name of executable for uncompression utility to use.
- : Will supercede those in @UNCOMPRESSION_UTILS defined by
+ : Will supersede those in @UNCOMPRESSION_UTILS defined by
: this module. If the absolute path to the executable is not provided,
: it will be searched in the PATH env variable.
Throws : Exception if file cannot be uncompressed.
@@ -882,7 +882,7 @@ sub create_filehandle {
: -FILE =>'usr/people/me/data.txt')
Argument : Same arguemnts as for create_filehandle().
Returns : Reference to a FileHandle object.
- Throws : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().
+ Throws : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline().
See Also : L<taste_file()|taste_file>, L<create_filehandle()|create_filehandle>
@@ -1039,7 +1039,7 @@ sub taste_file {
: mac (\r or 015 or ^M)
: unknown
Throws : Exception if argument is not a file
- : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline().
+ : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline().
See Also : L<get_newline()|get_newline>, L<taste_file()|taste_file>
diff --git a/Bio/Root/Version.pm b/Bio/Root/Version.pm
index e7bd376..27c1fdd 100644
--- a/Bio/Root/Version.pm
+++ b/Bio/Root/Version.pm
@@ -36,7 +36,7 @@ variable set if it's not already.
=cut
-our $VERSION = '1.007001';
+our $VERSION = '1.007002';
sub import {
# try to handle multiple levels of inheritance:
diff --git a/Bio/Search/BlastUtils.pm b/Bio/Search/BlastUtils.pm
index 6f756a0..6ae384c 100644
--- a/Bio/Search/BlastUtils.pm
+++ b/Bio/Search/BlastUtils.pm
@@ -486,7 +486,7 @@ sub collapse_nums {
: be a standard, the structure of the HTML-formatted version
: is even less so. Therefore, the use of this method to
: reconstitute parsable Blast reports from HTML-format versions
- : should be considered a temorary solution.
+ : should be considered a temporary solution.
=cut
diff --git a/Bio/Search/HSP/BlastPullHSP.pm b/Bio/Search/HSP/BlastPullHSP.pm
index 4f2e5c7..9eac701 100644
--- a/Bio/Search/HSP/BlastPullHSP.pm
+++ b/Bio/Search/HSP/BlastPullHSP.pm
@@ -396,7 +396,7 @@ sub gaps {
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
- 'list' or 'array' to retreive both query and hit together
+ 'list' or 'array' to retrieve both query and hit together
=cut
diff --git a/Bio/Search/HSP/GenericHSP.pm b/Bio/Search/HSP/GenericHSP.pm
index 23d1020..2989b0b 100644
--- a/Bio/Search/HSP/GenericHSP.pm
+++ b/Bio/Search/HSP/GenericHSP.pm
@@ -137,7 +137,7 @@ use base qw(Bio::Search::HSP::HSPI);
-identical => # of residues that that matched identically
-percent_identity => (optional) percent identity
-conserved => # of residues that matched conservatively
- (only protein comparisions;
+ (only protein comparisons;
conserved == identical in nucleotide comparisons)
-hsp_gaps => # of gaps in the HSP
-query_gaps => # of gaps in the query in the alignment
diff --git a/Bio/Search/HSP/HMMERHSP.pm b/Bio/Search/HSP/HMMERHSP.pm
index 70b2ef0..9eead34 100644
--- a/Bio/Search/HSP/HMMERHSP.pm
+++ b/Bio/Search/HSP/HMMERHSP.pm
@@ -91,7 +91,7 @@ Plus Bio::Search::HSP::GenericHSP methods
-hsp_length => Length of the HSP (including gaps)
-identical => # of residues that that matched identically
-conserved => # of residues that matched conservatively
- (only protein comparisions -
+ (only protein comparisons -
conserved == identical in nucleotide comparisons)
-hsp_gaps => # of gaps in the HSP
-query_gaps => # of gaps in the query in the alignment
diff --git a/Bio/Search/HSP/HSPI.pm b/Bio/Search/HSP/HSPI.pm
index 171db0d..a28b0c9 100644
--- a/Bio/Search/HSP/HSPI.pm
+++ b/Bio/Search/HSP/HSPI.pm
@@ -454,7 +454,7 @@ These methods come from L<Bio::SeqFeature::SimilarityPair>
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
- 'list' or 'array' to retreive both query and hit together
+ 'list' or 'array' to retrieve both query and hit together
=cut
diff --git a/Bio/Search/HSP/ModelHSP.pm b/Bio/Search/HSP/ModelHSP.pm
index 0ea0084..c83905b 100644
--- a/Bio/Search/HSP/ModelHSP.pm
+++ b/Bio/Search/HSP/ModelHSP.pm
@@ -97,7 +97,7 @@ Plus Bio::Seach::HSP::ModelHSP methods
-hsp_length=> Length of the HSP (including gaps)
-identical => # of residues that that matched identically
-conserved => # of residues that matched conservatively
- (only protein comparisions;
+ (only protein comparisons;
conserved == identical in nucleotide comparisons)
-hsp_gaps => # of gaps in the HSP
-query_gaps => # of gaps in the query in the alignment
diff --git a/Bio/Search/HSP/PullHSPI.pm b/Bio/Search/HSP/PullHSPI.pm
index 363a5d0..7a3ee0a 100755
--- a/Bio/Search/HSP/PullHSPI.pm
+++ b/Bio/Search/HSP/PullHSPI.pm
@@ -651,7 +651,7 @@ sub bits {
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
- 'list' or 'array' to retreive both query and hit together
+ 'list' or 'array' to retrieve both query and hit together
=cut
diff --git a/Bio/Search/Hit/GenericHit.pm b/Bio/Search/Hit/GenericHit.pm
index bc23088..cc6e42f 100644
--- a/Bio/Search/Hit/GenericHit.pm
+++ b/Bio/Search/Hit/GenericHit.pm
@@ -281,7 +281,7 @@ sub accession {
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
- Args : [optional] scalar string to set the descrition
+ Args : [optional] scalar string to set the description
=cut
diff --git a/Bio/Search/Hit/HMMERHit.pm b/Bio/Search/Hit/HMMERHit.pm
index b04776e..d16e4a7 100644
--- a/Bio/Search/Hit/HMMERHit.pm
+++ b/Bio/Search/Hit/HMMERHit.pm
@@ -173,7 +173,7 @@ sub domains{ shift->hsps() }
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
- Args : [optional] scalar string to set the descrition
+ Args : [optional] scalar string to set the description
=cut
diff --git a/Bio/Search/Hit/ModelHit.pm b/Bio/Search/Hit/ModelHit.pm
index a1f3233..e6b8c21 100644
--- a/Bio/Search/Hit/ModelHit.pm
+++ b/Bio/Search/Hit/ModelHit.pm
@@ -171,7 +171,7 @@ Implementation of Bio::Search::Hit::HitI methods
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
- Args : [optional] scalar string to set the descrition
+ Args : [optional] scalar string to set the description
=cut
diff --git a/Bio/Search/Iteration/IterationI.pm b/Bio/Search/Iteration/IterationI.pm
index c6fe71b..59fbc54 100644
--- a/Bio/Search/Iteration/IterationI.pm
+++ b/Bio/Search/Iteration/IterationI.pm
@@ -154,7 +154,7 @@ are still not below threshold in the current iteration.
=item * oldhits() [subset C]
-All hits that occured in a previous iteration, whether below or above
+All hits that occurred in a previous iteration, whether below or above
threshold in the current iteration. Union of oldhits_below_threshold()
+ oldhits_newly_below_threshold() + oldhits_not_below_threshold()
[subset H + subset I + subset G]. (Not applicable to the first
diff --git a/Bio/Search/SearchUtils.pm b/Bio/Search/SearchUtils.pm
index 57d44a9..dee7351 100644
--- a/Bio/Search/SearchUtils.pm
+++ b/Bio/Search/SearchUtils.pm
@@ -703,7 +703,7 @@ sub collapse_nums {
: be a standard, the structure of the HTML-formatted version
: is even less so. Therefore, the use of this method to
: reconstitute parsable Blast reports from HTML-format versions
- : should be considered a temorary solution.
+ : should be considered a temporary solution.
=cut
diff --git a/Bio/Search/Tiling/TilingI.pm b/Bio/Search/Tiling/TilingI.pm
index 092a4b1..6ef9c3c 100755
--- a/Bio/Search/Tiling/TilingI.pm
+++ b/Bio/Search/Tiling/TilingI.pm
@@ -19,7 +19,7 @@ Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
Not used directly. Useful POD here for developers, however.
-The interface is desgined to make the following code conversion as
+The interface is designed to make the following code conversion as
simple as possible:
From:
diff --git a/Bio/SearchDist.pm b/Bio/SearchDist.pm
index fde1631..1cc8ca9 100644
--- a/Bio/SearchDist.pm
+++ b/Bio/SearchDist.pm
@@ -48,7 +48,7 @@ The fitting procedure is better described in Sean Eddy's own code
file in Compile/SW). Bascially it fits a EVD via a maximum likelhood
method with pruning of the top end of the distribution so that real
positives are discarded in the fitting procedure. This comes from
-an orginally idea of Richard Mott's and the likelhood fitting
+an originally idea of Richard Mott's and the likelhood fitting
is from a book by Lawless [should ref here].
diff --git a/Bio/SearchIO.pm b/Bio/SearchIO.pm
index 9fd06d8..bf94084 100644
--- a/Bio/SearchIO.pm
+++ b/Bio/SearchIO.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::SearchIO
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
@@ -13,7 +13,7 @@
=head1 NAME
-Bio::SearchIO - Driver for parsing Sequence Database Searches
+Bio::SearchIO - Driver for parsing Sequence Database Searches
(BLAST, FASTA, ...)
=head1 SYNOPSIS
@@ -25,7 +25,7 @@ Bio::SearchIO - Driver for parsing Sequence Database Searches
while ( my $result = $searchio->next_result() ) {
while( my $hit = $result->next_hit ) {
# process the Bio::Search::Hit::HitI object
- while( my $hsp = $hit->next_hsp ) {
+ while( my $hsp = $hit->next_hsp ) {
# process the Bio::Search::HSP::HSPI object
}
}
@@ -46,7 +46,7 @@ represents one Blast/Fasta/HMMER whatever report.
A list of module names and formats is below:
- blast BLAST (WUBLAST, NCBIBLAST,bl2seq)
+ blast BLAST (WUBLAST, NCBIBLAST,bl2seq)
fasta FASTA -m9 and -m0
blasttable BLAST -m9 or -m8 output (both NCBI and WUBLAST tabular)
megablast MEGABLAST
@@ -60,7 +60,7 @@ A list of module names and formats is below:
wise Genewise -genesf format
Also see the SearchIO HOWTO:
-http://bioperl.open-bio.org/wiki/HOWTO:SearchIO
+http://bioperl.org/howtos/SearchIO_HOWTO.html
=head1 FEEDBACK
@@ -73,15 +73,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -129,7 +129,7 @@ use base qw(Bio::Root::IO Bio::Event::EventGeneratorI Bio::AnalysisParserI);
Title : new
Usage : my $obj = Bio::SearchIO->new();
- Function: Builds a new Bio::SearchIO object
+ Function: Builds a new Bio::SearchIO object
Returns : Bio::SearchIO initialized with the correct format
Args : -file => $filename
-format => format
@@ -178,14 +178,14 @@ default ones if none are supplied as arguments.
sub new {
my($caller, at args) = @_;
my $class = ref($caller) || $caller;
-
+
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::SearchIO::(\S+)/ ) {
- my ($self) = $class->SUPER::new(@args);
+ my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
- } else {
+ } else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
@@ -212,7 +212,7 @@ sub new {
# normalize capitalization to lower case
$format = "\L$format";
-
+
return unless( $class->_load_format_module($format) );
return "Bio::SearchIO::${format}"->new(@args);
}
@@ -374,7 +374,7 @@ sub next_result {
Title : write_result
Usage : $stream->write_result($result_result, @other_args)
Function: Writes data from the $result_result object into the stream.
- : Delegates to the to_string() method of the associated
+ : Delegates to the to_string() method of the associated
: WriterI object.
Returns : 1 for success and 0 for error
Args : Bio::Search:Result::ResultI object,
@@ -396,7 +396,7 @@ sub write_result {
my $str = $self->writer->to_string( $result, @args);
$self->{'_notfirsttime'} = 1;
$self->_print( "$str" ) if defined $str;
-
+
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
@@ -429,7 +429,7 @@ sub write_report {
my $str = $self->writer->to_string( $result, @args);
$self->{'_notfirsttime'} = 1;
$self->_print( "$str" ) if defined $str;
-
+
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
@@ -480,10 +480,10 @@ sub result_count {
Title : inclusion_threshold
Usage : my $incl_thresh = $isreb->inclusion_threshold;
: $isreb->inclusion_threshold(1e-5);
- Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
+ Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
score matrix model (blastpgp) that was used for generating the reports
being parsed.
- Returns : number (real)
+ Returns : number (real)
Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
Args : number (real) (e.g., 0.0001 or 1e-4 )
@@ -503,7 +503,7 @@ sub inclusion_threshold {
Returns : Scientific notation number with this format: 1.0e-05.
Argument : Scientific notation number or float (when setting)
Comments : Screening of significant hits uses the data provided on the
- : description line. For NCBI BLAST1 and WU-BLAST, this data
+ : description line. For NCBI BLAST1 and WU-BLAST, this data
: is P-value. for NCBI BLAST2 it is an Expect value.
=cut
@@ -527,7 +527,7 @@ sub signif { shift->max_significance(@_) }
Returns : Integer or scientific notation number.
Argument : Integer or scientific notation number (when setting)
Comments : Screening of significant hits uses the data provided on the
- : description line.
+ : description line.
=cut
@@ -567,7 +567,7 @@ sub min_query_length {
Title : best_hit_only
Usage : print "only getting best hit.\n" if $obj->best_hit_only;
- Purpose : Set/Get the indicator for whether or not to process only
+ Purpose : Set/Get the indicator for whether or not to process only
: the best BlastHit.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
@@ -586,7 +586,7 @@ sub best_hit_only {
Usage : print "checking all hits.\n" if $obj->check_all_hits;
Purpose : Set/Get the indicator for whether or not to process all hits.
: If false, the parser will stop processing hits after the
- : the first non-significance hit or the first hit that fails
+ : the first non-significance hit or the first hit that fails
: any hit filter.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
@@ -604,9 +604,9 @@ sub check_all_hits {
Title : _load_format_module
Usage : *INTERNAL SearchIO stuff*
Function: Loads up (like use) a module at run time on demand
- Example :
- Returns :
- Args :
+ Example :
+ Returns :
+ Args :
=cut
@@ -614,7 +614,7 @@ sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::SearchIO::" . $format;
my $ok;
-
+
eval {
$ok = $self->_load_module($module);
};
@@ -703,8 +703,8 @@ sub _guess_format {
return 'exonerate' if ( /\.exon(erate)?/i );
}
-sub close {
- my $self = shift;
+sub close {
+ my $self = shift;
if( $self->writer ) {
$self->_print($self->writer->end_report());
diff --git a/Bio/SearchIO/Writer/HTMLResultWriter.pm b/Bio/SearchIO/Writer/HTMLResultWriter.pm
index 488f804..c992a2b 100644
--- a/Bio/SearchIO/Writer/HTMLResultWriter.pm
+++ b/Bio/SearchIO/Writer/HTMLResultWriter.pm
@@ -438,7 +438,7 @@ sub to_string {
if( defined $v->{'start'} ) {
$start = $v->{'start'};
# since strand can be + or - use the direction
- # to signify which whether to add or substract from end
+ # to signify which whether to add or subtract from end
my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )*
$baselens{$v->{'name'}};
if( length($piece) < $AlignmentLineWidth ) {
diff --git a/Bio/SearchIO/Writer/TextResultWriter.pm b/Bio/SearchIO/Writer/TextResultWriter.pm
index d6c1b9d..411d638 100644
--- a/Bio/SearchIO/Writer/TextResultWriter.pm
+++ b/Bio/SearchIO/Writer/TextResultWriter.pm
@@ -416,7 +416,7 @@ Sequences producing significant alignments: (bits) value
if( defined $v->{'start'} ) {
$start = $v->{'start'};
# since strand can be + or - use the direction
- # to signify which whether to add or substract from end
+ # to signify which whether to add or subtract from end
my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )*
$baselens{$v->{'name'}};
if( length($piece) < $AlignmentLineWidth ) {
diff --git a/Bio/SearchIO/exonerate.pm b/Bio/SearchIO/exonerate.pm
index 9d96dff..c207967 100644
--- a/Bio/SearchIO/exonerate.pm
+++ b/Bio/SearchIO/exonerate.pm
@@ -164,7 +164,7 @@ $MIN_INTRON=30; # This is the minimum intron size
Usage : my $obj = Bio::SearchIO::exonerate->new();
Function: Builds a new Bio::SearchIO::exonerate object
Returns : an instance of Bio::SearchIO::exonerate
- Args : -min_intron => somewhat obselete option, how to determine if a
+ Args : -min_intron => somewhat obsolete option, how to determine if a
an indel is an intron or a local gap. Use VULGAR
rather than CIGAR to avoid this heuristic,default 30.
-cigar => 1 set this to 1 if you want to parse
diff --git a/Bio/SearchIO/fasta.pm b/Bio/SearchIO/fasta.pm
index 5fb85f1..f920941 100644
--- a/Bio/SearchIO/fasta.pm
+++ b/Bio/SearchIO/fasta.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::SearchIO::fasta
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
@@ -29,13 +29,13 @@ Bio::SearchIO::fasta - A SearchIO parser for FASTA results
This object contains the event based parsing code for FASTA format
reports. It creates L<Bio::Search::HSP::FastaHSP> objects instead of
-L<Bio::Search::HSP::GenericHSP> for the HSP objects.
+L<Bio::Search::HSP::GenericHSP> for the HSP objects.
This module will parse -m 9 -d 0 output as well as default m 1 output
from FASTA as well as SSEARCH.
Also see the SearchIO HOWTO:
-L<http://bioperl.open-bio.org/wiki/HOWTO:SearchIO>.
+L<http://bioperl.org/howtos/SearchIO_HOWTO.html>.
=head1 FEEDBACK
@@ -48,15 +48,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -170,9 +170,9 @@ use base qw(Bio::SearchIO);
Title : new
Usage : my $obj = Bio::SearchIO::fasta->new();
- Function: Builds a new Bio::SearchIO::fasta object
+ Function: Builds a new Bio::SearchIO::fasta object
Returns : Bio::SearchIO::fasta
- Args : -idlength - set ID length to something other
+ Args : -idlength - set ID length to something other
than the default (6), this is only
necessary if you have compiled FASTA
with a new default id length to display
@@ -488,7 +488,7 @@ sub next_result {
} elsif ($_ eq "E2()") {
$_ = "evalue2";
}
-
+
$_;
}
} @labels[ $rel ? 5 : 4 .. $#labels ];
@@ -507,12 +507,12 @@ sub next_result {
$m9HSP = 1;
# parse HSP, add to last parsed Hit
my %hspData;
-
+
my @line = split;
@hspData{@labels} = splice( @line, @line - @labels );
$hspData{lframe} = $hit_signifs[-1]->{lframe};
-
+
push @{$hit_signifs[-1]->{HSPs}}, \%hspData;
next;
@@ -557,7 +557,7 @@ sub next_result {
@data{qw(id desc acc)} = ( $id, $desc, $acc );
$data{HSPs} = [ \%hspData ];
-
+
push @hit_signifs, \%data;
}
}
@@ -683,7 +683,7 @@ sub next_result {
if ( $self->in_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
-
+
my $firstHSP = 0;
if ($1 ne ">--") {
$firstHSP = 1;
@@ -706,7 +706,7 @@ sub next_result {
$self->end_element( { 'Name' => 'Hit' } );
shift @hit_signifs if @hit_signifs;
}
-
+
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
@@ -721,7 +721,7 @@ sub next_result {
'Data' => $id
}
);
-
+
#$self->debug("Hit ID is $id\n");
my @pieces = split( /\|/, $id );
my $acc = pop @pieces;
@@ -781,7 +781,7 @@ sub next_result {
}
);
}
-
+
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
@@ -986,7 +986,7 @@ sub next_result {
}
$self->_processHits(@hit_signifs) if @hit_signifs;
-
+
$self->end_element( { 'Name' => 'FastaOutput' } );
return $self->end_document();
}
@@ -1002,7 +1002,7 @@ sub next_result {
}
$self->_processHits(@hit_signifs) if (@hit_signifs);
-
+
$self->end_element( { 'Name' => 'FastaOutput' } );
$self->_pushback($_);
return $self->end_document();
@@ -1353,8 +1353,8 @@ sub characters {
Title : _mode
Usage : $obj->_mode($newval)
- Function:
- Example :
+ Function:
+ Example :
Returns : value of _mode
Args : newvalue (optional)
@@ -1377,7 +1377,7 @@ sub _mode {
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
- Args : string element name
+ Args : string element name
=cut
@@ -1403,7 +1403,7 @@ sub within_element {
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
- Args : string element name
+ Args : string element name
=cut
@@ -1507,7 +1507,7 @@ sub attach_EventHandler {
Title : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
- Function: Provides an optimized way to check whether or not an element of a
+ Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
diff --git a/Bio/SearchIO/hmmer3.pm b/Bio/SearchIO/hmmer3.pm
index 3549817..0ff6b2c 100644
--- a/Bio/SearchIO/hmmer3.pm
+++ b/Bio/SearchIO/hmmer3.pm
@@ -1244,7 +1244,7 @@ sub end_document {
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results processed
- Returns : interger
+ Returns : integer
Args : none
=cut
diff --git a/Bio/Seq.pm b/Bio/Seq.pm
index 0b020e0..348f6c6 100644
--- a/Bio/Seq.pm
+++ b/Bio/Seq.pm
@@ -69,7 +69,7 @@ Bio::Seq - Sequence object, with features
# you can get truncations, translations and reverse complements, these
# all give back Bio::Seq objects themselves, though currently with no
- # features transfered
+ # features transferred
my $trunc = $seqobj->trunc(100,200);
my $rev = $seqobj->revcom();
@@ -669,7 +669,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
- unique id for the implemetation, allowing multiple objects
+ unique id for the implementation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
@@ -889,7 +889,7 @@ sub namespace{
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
- user of this interface would not assumme this) and should be
+ user of this interface would not assume this) and should be
less than thirty characters (though again, double checking
this is a good idea)
diff --git a/Bio/Seq/EncodedSeq.pm b/Bio/Seq/EncodedSeq.pm
index cad3bd8..bf9f092 100644
--- a/Bio/Seq/EncodedSeq.pm
+++ b/Bio/Seq/EncodedSeq.pm
@@ -175,7 +175,7 @@ use base qw(Bio::LocatableSeq);
gap ('G') or backward frameshift ('B') should
have one or more gap characters; if the encoding
specifies G or B, but no (or not enough) gap
- characters exist, *they'll be added*; similary,
+ characters exist, *they'll be added*; similarly,
if there are gap characters without a
corresponding G or B encoding, G's will be
inserted into the encoding. This allows some
diff --git a/Bio/Seq/Meta/Array.pm b/Bio/Seq/Meta/Array.pm
index 9f1c035..9a65f70 100644
--- a/Bio/Seq/Meta/Array.pm
+++ b/Bio/Seq/Meta/Array.pm
@@ -343,7 +343,7 @@ sub named_meta_text {
should extend to the end of the sequence.
The return value may be a string or an array reference,
- depending on the implentation. If in doubt, use
+ depending on the implementation. If in doubt, use
submeta_text() which is a variant guarantied to return a
string. See L<submeta_text>.
@@ -469,7 +469,7 @@ sub named_submeta_text {
Title : meta_names
Usage : @meta_names = $obj->meta_names()
- Function: Retrives an array of meta data set names. The default
+ Function: Retrieves an array of meta data set names. The default
(unnamed) set name is guarantied to be the first name if it
contains any data.
Returns : an array of names
diff --git a/Bio/Seq/MetaI.pm b/Bio/Seq/MetaI.pm
index 221615f..daf8fa5 100644
--- a/Bio/Seq/MetaI.pm
+++ b/Bio/Seq/MetaI.pm
@@ -180,7 +180,7 @@ use base qw(Bio::Root::RootI);
(reference).
The return value may be a string or an array reference,
- depending on the implentation. If in doubt, use meta_text()
+ depending on the implementation. If in doubt, use meta_text()
which is a variant guarantied to return a string. See
L<meta_text>.
@@ -256,7 +256,7 @@ sub named_meta_text { shift->throw_not_implemented }
sequence, they should be ignored.
The return value may be a string or an array reference,
- depending on the implentation. If in doubt, use
+ depending on the implementation. If in doubt, use
submeta_text() which is a variant guarantied to return a
string. See L<submeta_text>.
@@ -321,7 +321,7 @@ sub named_submeta_text { shift->throw_not_implemented }
Title : meta_names
Usage : @meta_names = $obj->meta_names()
- Function: Retrives an array of meta data set names. The default (unnamed)
+ Function: Retrieves an array of meta data set names. The default (unnamed)
set name is guarantied to be the first name.
Returns : an array of names
Args : none
@@ -389,7 +389,7 @@ sub named_meta_length { shift->throw_not_implemented }
=head1 Bio::PrimarySeqI methods
-Implemeting classes will need to rewrite these Bio::PrimaryI methods.
+Implementing classes will need to rewrite these Bio::PrimaryI methods.
=cut
diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm
index 4709a2a..6a93d34 100644
--- a/Bio/Seq/PrimaryQual.pm
+++ b/Bio/Seq/PrimaryQual.pm
@@ -327,7 +327,7 @@ sub header {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the unique id
- for the implemetation, allowing multiple objects to have the same
+ for the implementation, allowing multiple objects to have the same
accession number in a particular implementation. For sequences
with no accession number, this method should return "unknown".
Returns : A string
@@ -354,7 +354,7 @@ sub accession_number {
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
- way the implementaiton can control clients can expect one id to
+ way the implementation can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
Returns : A string
diff --git a/Bio/Seq/PrimedSeq.pm b/Bio/Seq/PrimedSeq.pm
index 0990a2a..7b18e7d 100644
--- a/Bio/Seq/PrimedSeq.pm
+++ b/Bio/Seq/PrimedSeq.pm
@@ -300,7 +300,7 @@ sub get_primer {
Title : annotated_sequence
Usage : my $annotated_sequence_object = $primedseq->annotate_sequence();
- Function: Get an annotated sequence object containg the left and right
+ Function: Get an annotated sequence object containing the left and right
primers
Returns : An annotated sequence object or 0 if not defined.
Args :
diff --git a/Bio/Seq/QualI.pm b/Bio/Seq/QualI.pm
index 27dedbd..ac6a909 100644
--- a/Bio/Seq/QualI.pm
+++ b/Bio/Seq/QualI.pm
@@ -211,7 +211,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the unique id
- for the implemetation, allowing multiple objects to have the same
+ for the implementation, allowing multiple objects to have the same
accession number in a particular implementation. For sequences
with no accession number, this method should return "unknown".
Returns : A string.
@@ -240,7 +240,7 @@ sub accession_number {
$unique_implementation_key = $obj->primary_id($new_prim_id);
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
- way the implementaiton can control clients can expect one id to
+ way the implementation can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
Returns : A string
@@ -331,8 +331,8 @@ are encouraged to override these methods
Usage : @rev = @{$qual->revcom()};
Function: Produces a new Bio::Seq::QualI implementing object which
is reversed from the original quality array.
- The id is the same id as the orginal sequence, and the accession number
- is also indentical. If someone wants to track that this sequence has
+ The id is the same id as the original sequence, and the accession number
+ is also identical. If someone wants to track that this sequence has
been reversed, it needs to define its own extensions
To do an inplace edit of an object you can go:
diff --git a/Bio/Seq/RichSeqI.pm b/Bio/Seq/RichSeqI.pm
index 59873f4..849014f 100644
--- a/Bio/Seq/RichSeqI.pm
+++ b/Bio/Seq/RichSeqI.pm
@@ -113,7 +113,7 @@ sub get_secondary_accessions{
Title : division
Usage :
- Function: Get (and set, depending on the implementation) the divison for
+ Function: Get (and set, depending on the implementation) the division for
a sequence.
Examples from GenBank are PLN (plants), PRI (primates), etc.
diff --git a/Bio/Seq/SeqBuilder.pm b/Bio/Seq/SeqBuilder.pm
index 551f3a8..9f201ad 100644
--- a/Bio/Seq/SeqBuilder.pm
+++ b/Bio/Seq/SeqBuilder.pm
@@ -355,7 +355,7 @@ sub make_object{
=head1 Implementation specific methods
-These methods allow to conveniently configure this sequence object
+These methods allow one to conveniently configure this sequence object
builder as to which slots are desired, and under which circumstances a
sequence object should be abandoned altogether. The default mode is
want_all(1), which means the builder will report all slots as wanted
@@ -564,7 +564,7 @@ sub want_all{
Conditions in this implementation are closures (anonymous
functions) which are passed one parameter, a hash reference
the keys of which are equal to initialization
- paramaters. The closure must return TRUE to make the object
+ parameters. The closure must return TRUE to make the object
'wanted.'
Conditions will be implicitly ANDed.
diff --git a/Bio/Seq/SeqWithQuality.pm b/Bio/Seq/SeqWithQuality.pm
index abdb137..fd7c77e 100644
--- a/Bio/Seq/SeqWithQuality.pm
+++ b/Bio/Seq/SeqWithQuality.pm
@@ -171,7 +171,7 @@ sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# default: turn OFF the warnings
- $self->{supress_warnings} = 1;
+ $self->{suppress_warnings} = 1;
my($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet,$trace_indices) =
$self->_rearrange([qw( QUAL SEQ DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID DESC
ID ALPHABET TRACE_INDICES )], @args);
@@ -188,7 +188,7 @@ sub new {
# Import sequence first
if (!$seq) {
my $id;
- unless ($self->{supress_warnings} == 1) {
+ unless ($self->{suppress_warnings} == 1) {
$self->warn("You did not provide sequence information during the ".
"construction of a Bio::Seq::SeqWithQuality object. Sequence ".
"components for this object will be empty.");
@@ -427,7 +427,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the unique id
- for the implemetation, allowing multiple objects to have the same
+ for the implementation, allowing multiple objects to have the same
accession number in a particular implementation. For sequences
with no accession number, this method should return "unknown".
This method sets the accession_number for the SeqWithQuality
@@ -457,7 +457,7 @@ sub accession_number {
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
- way the implementaiton can control clients can expect one id to
+ way the implementation can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the SeqWithQuality object.
@@ -632,13 +632,13 @@ sub trace_indices {
sub length {
my $self = shift;
if (!$self->{seq_ref}) {
- unless ($self->{supress_warnings} == 1) {
+ unless ($self->{suppress_warnings} == 1) {
$self->warn("Can't find {seq_ref} here in length().");
}
return;
}
if (!$self->{qual_ref}) {
- unless ($self->{supress_warnings} == 1) {
+ unless ($self->{suppress_warnings} == 1) {
$self->warn("Can't find {qual_ref} here in length().");
}
return;
@@ -646,7 +646,7 @@ sub length {
my $seql = $self->{seq_ref}->length();
if ($seql != $self->{qual_ref}->length()) {
- unless ($self->{supress_warnings} == 1) {
+ unless ($self->{suppress_warnings} == 1) {
$self->warn("Sequence length (".$seql.") is different from quality ".
"length (".$self->{qual_ref}->length().") in the SeqWithQuality ".
"object. This can only lead to problems later.");
diff --git a/Bio/Seq/SequenceTrace.pm b/Bio/Seq/SequenceTrace.pm
index 5f00549..ff78468 100755
--- a/Bio/Seq/SequenceTrace.pm
+++ b/Bio/Seq/SequenceTrace.pm
@@ -101,7 +101,7 @@ sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# default: turn OFF the warnings
- $self->{supress_warnings} = 1;
+ $self->{suppress_warnings} = 1;
my($swq,$peak_indices,$trace_a,$trace_t,
$trace_g,$trace_c,$acc_a,$acc_t,$acc_g,$acc_c) =
$self->_rearrange([qw(
@@ -343,7 +343,7 @@ sub display_id {
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the unique id
- for the implemetation, allowing multiple objects to have the same
+ for the implementation, allowing multiple objects to have the same
accession number in a particular implementation. For sequences
with no accession number, this method should return "unknown".
This method sets the accession_number for the Quality
@@ -373,7 +373,7 @@ sub accession_number {
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
- way the implementaiton can control clients can expect one id to
+ way the implementation can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the Quality
diff --git a/Bio/Seq/SimulatedRead.pm b/Bio/Seq/SimulatedRead.pm
index fcc381e..948749b 100644
--- a/Bio/Seq/SimulatedRead.pm
+++ b/Bio/Seq/SimulatedRead.pm
@@ -376,7 +376,7 @@ sub _update_desc_mid {
Substitutions and deletions are for a single residue, but additions
can be additions of several residues.
An alternative way to specify errors is by using array references
- instead of scalar for the hash values. This allows to specify
+ instead of scalar for the hash values. This allows one to specify
redundant mutations. For example, the case presented above would
result in the same read sequence as the example below:
$errors->{34}->{'%'} = ['C', 'T'] ; # substitution by a C and then a T
diff --git a/Bio/SeqFeature/AnnotationAdaptor.pm b/Bio/SeqFeature/AnnotationAdaptor.pm
index f3d9bc7..686f5e7 100644
--- a/Bio/SeqFeature/AnnotationAdaptor.pm
+++ b/Bio/SeqFeature/AnnotationAdaptor.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::SeqFeature::AnnotationAdaptor
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
@@ -17,7 +17,7 @@
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
-#
+#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
@@ -46,17 +46,17 @@ Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation
$feat->annotation->add_Annotation("dbxref", $dblink);
# to integrate tag/value annotation with AnnotationCollectionI
- # annotation, use this adaptor, which also implements
+ # annotation, use this adaptor, which also implements
# Bio::AnnotationCollectionI
my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat);
- # this will now return tag/value pairs as
+ # this will now return tag/value pairs as
# Bio::Annotation::SimpleValue objects
my @anns = $anncoll->get_Annotations("mytag");
# other added before annotation is available too
my @dblinks = $anncoll->get_Annotations("dbxref");
- # also supports transparent adding of tag/value pairs in
+ # also supports transparent adding of tag/value pairs in
# Bio::AnnotationI flavor
my $tagval = Bio::Annotation::SimpleValue->new(-value => "some value",
-tagname => "some tag");
@@ -107,15 +107,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -154,7 +154,7 @@ use base qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotatableI);
Title : new
Usage : my $obj = Bio::SeqFeature::AnnotationAdaptor->new();
- Function: Builds a new Bio::SeqFeature::AnnotationAdaptor object
+ Function: Builds a new Bio::SeqFeature::AnnotationAdaptor object
Returns : an instance of Bio::SeqFeature::AnnotationAdaptor
Args : Named parameters
-feature the Bio::SeqFeatureI implementing object to adapt
@@ -192,7 +192,7 @@ sub new {
Usage : $obj->feature($newval)
Function: Get/set the feature that this object adapts to an
AnnotationCollectionI.
- Example :
+ Example :
Returns : value of feature (a Bio::SeqFeatureI compliant object)
Args : new value (a Bio::SeqFeatureI compliant object, optional)
@@ -217,7 +217,7 @@ sub feature{
If requested before having been set, the value will default to the
annotation object of the feature if it has one.
- Example :
+ Example :
Returns : value of annotation (a Bio::AnnotationCollectionI compliant object)
Args : new value (a Bio::AnnotationCollectionI compliant object, optional)
@@ -254,7 +254,7 @@ sub annotation{
sub get_all_annotation_keys{
my ($self) = @_;
my @keys = ();
-
+
# get the tags from the feature object
if ($self->feature()->can('get_all_tags')) {
push(@keys, $self->feature()->get_all_tags());
@@ -322,7 +322,7 @@ sub get_Annotations{
Title : get_num_of_annotations
Usage : my $count = $collection->get_num_of_annotations()
- Function: Returns the count of all annotations stored in this collection
+ Function: Returns the count of all annotations stored in this collection
Returns : integer
Args : none
@@ -376,14 +376,14 @@ sub get_num_of_annotations{
Returns : none
Args : annotation key ('disease', 'dblink', ...)
object to store (must be Bio::AnnotationI compliant)
- [optional] object archetype to map future storage of object
+ [optional] object archetype to map future storage of object
of these types to
=cut
sub add_Annotation{
my ($self,$key,$object,$archetype) = @_;
-
+
# if there's no key we use the tagname() as key
if(ref($key) && $key->isa("Bio::AnnotationI") &&
(! ($object && ref($object)))) {
@@ -394,15 +394,15 @@ sub add_Annotation{
$self->throw("Annotation object must have a tagname if key omitted")
unless $key;
}
-
+
if( !defined $object ) {
$self->throw("Must have at least key and object in add_Annotation");
}
-
+
if( ! (ref($object) && $object->isa("Bio::AnnotationI")) ) {
- $self->throw("object must be a Bio::AnnotationI compliant object, otherwise we wont add it!");
+ $self->throw("object must be a Bio::AnnotationI compliant object, otherwise we won't add it!");
}
-
+
# ready to add -- if it's a SimpleValue, we add to the feature's tags,
# otherwise we'll add to the annotation collection implementation
@@ -453,7 +453,7 @@ sub remove_Annotations{
foreach my $key (@keys) {
# delete the tag if it is one
$self->feature->remove_tag($key) if $self->feature->has_tag($key);
- # and delegate to the annotation implementation
+ # and delegate to the annotation implementation
my $anncoll = $self->annotation();
if($anncoll && $anncoll->can('remove_Annotations')) {
$anncoll->remove_Annotations($key);
@@ -481,9 +481,9 @@ sub remove_Annotations{
Bio::Annotation::SimpleValue in terms of supported
arguments at creation time, and the methods.
- Example :
+ Example :
Returns : A Bio::Factory::ObjectFactoryI compliant object
- Args : new value (a Bio::Factory::ObjectFactoryI compliant object,
+ Args : new value (a Bio::Factory::ObjectFactoryI compliant object,
optional)
diff --git a/Bio/SeqFeature/Computation.pm b/Bio/SeqFeature/Computation.pm
index 6c02630..189eba2 100644
--- a/Bio/SeqFeature/Computation.pm
+++ b/Bio/SeqFeature/Computation.pm
@@ -39,7 +39,7 @@ more types of score and subseqfeatures. It is compatible with the Generic
SeqFeature object.
The new way of storing score values is similar to the tag structure in the
-Generic object. For storing sets of subseqfeatures the array containg the
+Generic object. For storing sets of subseqfeatures the array containing the
subseqfeatures is now a hash which contains arrays of seqfeatures
Both the score and subSeqfeature methods can be called in exactly the same
way, the value's will be stored as a 'default' score or subseqfeature.
@@ -133,7 +133,7 @@ sub new {
Title : has_score
Usage : $value = $self->has_score('some_score')
- Function: Tests wether a feature contains a score
+ Function: Tests whether a feature contains a score
Returns : TRUE if the SeqFeature has the score,
and FALSE otherwise.
Args : The name of a score
@@ -463,7 +463,7 @@ sub get_all_SeqFeature_types {
Usage : @feats = $feat->get_SeqFeatures();
@feats = $feat->get_SeqFeatures('feature_type');
Function: Returns an array of sub Sequence Features of a specific
- type or, if the type is ommited, all sub Sequence Features
+ type or, if the type is omitted, all sub Sequence Features
Returns : An array
Args : (optional) a SeqFeature type (ie exon, pattern)
diff --git a/Bio/SeqFeature/Generic.pm b/Bio/SeqFeature/Generic.pm
index 772d5fe..c4564e5 100644
--- a/Bio/SeqFeature/Generic.pm
+++ b/Bio/SeqFeature/Generic.pm
@@ -46,7 +46,7 @@ the information for a feature on a sequence.
For many Features, this is all you will need to use (for example, this
is fine for Repeats in DNA sequence or Domains in protein
sequence). For other features, which have more structure, this is a
-good base class to extend using inheritence to have new things: this
+good base class to extend using inheritance to have new things: this
is what is done in the L<Bio::SeqFeature::Gene>,
L<Bio::SeqFeature::Transcript> and L<Bio::SeqFeature::Exon>, which provide
well coordinated classes to represent genes on DNA sequence (for
@@ -553,7 +553,7 @@ sub source_tag {
Title : has_tag
Usage : my $value = $feat->has_tag('some_tag');
- Function: Tests wether a feature contaings a tag
+ Function: Tests whether a feature containings a tag
Returns : TRUE if the SeqFeature has the tag,
and FALSE otherwise.
Args : The name of a tag
diff --git a/Bio/SeqFeature/Lite.pm b/Bio/SeqFeature/Lite.pm
index e74a5da..ed8885b 100644
--- a/Bio/SeqFeature/Lite.pm
+++ b/Bio/SeqFeature/Lite.pm
@@ -445,7 +445,7 @@ sub display_name { shift->name(@_) }
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
- unique id for the implemetation, allowing multiple objects
+ unique id for the implementation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
diff --git a/Bio/SeqFeature/PositionProxy.pm b/Bio/SeqFeature/PositionProxy.pm
index 54c4275..aa1f235 100644
--- a/Bio/SeqFeature/PositionProxy.pm
+++ b/Bio/SeqFeature/PositionProxy.pm
@@ -65,7 +65,7 @@ Ewan Birney E<lt>birney at sanger.ac.ukE<gt>
=head1 DEVELOPERS
-This class has been written with an eye out of inheritence. The fields
+This class has been written with an eye out of inheritance. The fields
the actual object hash are:
_gsf_tag_hash = reference to a hash for the tags
diff --git a/Bio/SeqFeature/SubSeq.pm b/Bio/SeqFeature/SubSeq.pm
index 465135b..296a406 100644
--- a/Bio/SeqFeature/SubSeq.pm
+++ b/Bio/SeqFeature/SubSeq.pm
@@ -36,7 +36,7 @@ Bio::SeqFeature::SubSeq extends L<Bio::SeqFeature::Generic> features to
represent a subsequence. When this feature is attached to a template sequence,
the sequence of feature is the subsequence of the template at this location. The
purpose of this class is to represent a sequence as a feature without having to
-explictly store its sequence string.
+explicitly store its sequence string.
Of course, you might have reasons to explicitly set a sequence. In that case,
note that the length of the sequence is allowed to not match the position of the
diff --git a/Bio/SeqFeature/Tools/Unflattener.pm b/Bio/SeqFeature/Tools/Unflattener.pm
index bf7e0cb..5cfc7fb 100644
--- a/Bio/SeqFeature/Tools/Unflattener.pm
+++ b/Bio/SeqFeature/Tools/Unflattener.pm
@@ -410,7 +410,7 @@ Occasionally a GenBank entry will have both implicit exons (from the
mRNA location) B<and> explicit exon features.
In this case, exons will still be transferred. Tag-value data from the
-explicit exon will be transfered to the implicit exon. If exons are
+explicit exon will be transferred to the implicit exon. If exons are
shared between mRNAs these will be represented by different
objects. Any inconsistencies between implicit and explicit will be
reported.
diff --git a/Bio/SeqFeature/TypedSeqFeatureI.pm b/Bio/SeqFeature/TypedSeqFeatureI.pm
index 5acd140..1bb2165 100644
--- a/Bio/SeqFeature/TypedSeqFeatureI.pm
+++ b/Bio/SeqFeature/TypedSeqFeatureI.pm
@@ -48,7 +48,7 @@ all the Bio::SeqFeatureI interface as well).
It is suggested that the primary_tag() method of SeqFeatureI
return the same as the ontology_term()-E<gt>name() of the OntologyTypedI
(ie, the "string" name of the ontology type is used as the primary
-tag), but this should not be assummed by client code as they
+tag), but this should not be assumed by client code as they
are scenarios where one would like to maintain the difference.
diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index a855249..5926b67 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -1,6 +1,6 @@
# BioPerl module for Bio::SeqIO
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Ewan Birney <birney at ebi.ac.uk>
# and Lincoln Stein <lstein at cshl.org>
@@ -190,7 +190,7 @@ Filehandles can also be used to read from or write to a piped command:
my $out=Bio::SeqIO->new(-file=>'>seq.fasta',
-format=>'fasta');
while (my $seq=$in->next_seq) {
- $out->write_seq($seq)
+ $out->write_seq($seq)
}
=item -string
@@ -205,12 +205,12 @@ A string to read the sequences from. For example:
Specify the format of the file. Supported formats include fasta,
genbank, embl, swiss (SwissProt), Entrez Gene and tracefile formats
such as abi (ABI) and scf. There are many more, for a complete listing
-see the SeqIO HOWTO (L<http://bioperl.open-bio.org/wiki/HOWTO:SeqIO>).
+see the SeqIO HOWTO (L<http://bioperl.org/howtos/SeqIO_HOWTO.html>).
If no format is specified and a filename is given then the module will
attempt to deduce the format from the filename suffix. If there is no
suffix that Bioperl understands then it will attempt to guess the
-format based on file content. If this is unsuccessful then SeqIO will
+format based on file content. If this is unsuccessful then SeqIO will
throw a fatal error.
The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta' are
@@ -303,15 +303,15 @@ Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
bioperl-l at bioperl.org
-rather than to the module maintainer directly. Many experienced and
-responsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+responsive 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
@@ -395,11 +395,11 @@ sub new {
unless( defined $params{-file} ||
defined $params{-fh} ||
defined $params{-string} ) {
- $class->throw("file argument provided, but with an undefined value")
+ $class->throw("file argument provided, but with an undefined value")
if exists $params{'-file'};
- $class->throw("fh argument provided, but with an undefined value")
+ $class->throw("fh argument provided, but with an undefined value")
if exists $params{'-fh'};
- $class->throw("string argument provided, but with an undefined value")
+ $class->throw("string argument provided, but with an undefined value")
if exists($params{'-string'});
# $class->throw("No file, fh, or string argument provided"); # neither defined
}
@@ -505,7 +505,7 @@ sub _initialize {
# note that this should come last because it propagates the sequence
# factory to the sequence builder
$seqfact && $self->sequence_factory($seqfact);
-
+
#bug 2160
$alphabet && $self->alphabet($alphabet);
diff --git a/Bio/SeqIO/ace.pm b/Bio/SeqIO/ace.pm
index 99ecd70..c5734f2 100644
--- a/Bio/SeqIO/ace.pm
+++ b/Bio/SeqIO/ace.pm
@@ -24,7 +24,7 @@ from ace file format. It only parses a DNA or
Peptide objects contained in the ace file,
producing PrimarySeq objects from them. All
other objects in the files will be ignored. It
-doesn't attempt to parse any annotation attatched
+doesn't attempt to parse any annotation attached
to the containing Sequence or Protein objects,
which would probably be impossible, since
everyone's ACeDB schema can be different.
diff --git a/Bio/SeqIO/bsml.pm b/Bio/SeqIO/bsml.pm
index 0ea41ed..6e48cbc 100644
--- a/Bio/SeqIO/bsml.pm
+++ b/Bio/SeqIO/bsml.pm
@@ -162,13 +162,16 @@ my $nvtoken = ": "; # The token used if a name/value pair has to be stuffed
=cut
-# LS: this seems to get overwritten on line 1317, generating a redefinition error. Dead code?
-# CAT: This was inappropriately added in revision 1.10 - I added the check for existance of a sequence factory to the actual _initialize
+# LS: this seems to get overwritten on line 1317, generating a redefinition error.
+# Dead code?
+# CAT: This was inappropriately added in revision 1.10 - I added the check for
+# existence of a sequence factory to the actual _initialize
# sub _initialize {
# my($self, at args) = @_;
# $self->SUPER::_initialize(@args);
# if( ! defined $self->sequence_factory ) {
-# $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq'));
+# $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(),
+# -type => 'Bio::Seq::RichSeq'));
# }
# }
@@ -608,7 +611,12 @@ sub to_bsml {
my $seqRefs = []; my $featRefs = [];
# Array references to hold <Attribute> values (not objects):
my $seqDesc = [];
- push @{$seqDesc}, ["comment" , "This file generated to BSML 2.2 standards - joins will be collapsed to a single feature enclosing all members of the join"];
+ push @{$seqDesc},
+ [
+ "comment",
+ "This file generated to BSML 2.2 standards - " .
+ "joins will be collapsed to a single feature enclosing all members of the join"
+ ];
push @{$seqDesc}, ["description" , eval{$bioSeq->desc}];
for my $kwd ( eval{$bioSeq->get_keywords} ) {
push @{$seqDesc}, ["keyword" , $kwd];
@@ -749,7 +757,7 @@ sub to_bsml {
next if (defined $args->{SKIPTAGS} &&
$args->{SKIPTAGS} =~ /all/i);
# Tags can consume a lot of CPU cycles, and can often be
- # rather non-informative, so -skiptags can allow total or
+ # rather non-informative, so -skiptags can allow one total or
# selective omission of tags.
for my $tag ($bioFeat->all_tags()) {
next if (exists $args->{SKIPTAGS}{$tag});
@@ -833,7 +841,7 @@ sub to_bsml {
document, where $mimetype is the value designated by this
key. For generic XML use text/xml, for BSML use text/x-bsml
- -return This option will be supressed, since the nature of this
+ -return This option will be suppressed, since the nature of this
method is to print out the XML document. If you wish to
retrieve the <Sequence> objects generated, use the to_bsml
method directly.
diff --git a/Bio/SeqIO/chadoxml.pm b/Bio/SeqIO/chadoxml.pm
index 707fd4e..ccdee71 100644
--- a/Bio/SeqIO/chadoxml.pm
+++ b/Bio/SeqIO/chadoxml.pm
@@ -348,7 +348,7 @@ GenBank data file for a Drosophila melanogaster genome scaffold has the molecule
type of "DNA", when converting to chadoxml, a $seqSOtype argument of
"golden_path_region" can be supplied to save the scaffold as a feature of type
"golden_path_region" in chadoxml, instead of "DNA". a feature with primary tag
-of 'source' must be present in the sequence feature list of $seq, to decribe the
+of 'source' must be present in the sequence feature list of $seq, to describe the
whole sequence record.
In the current implementation:
@@ -495,7 +495,7 @@ EOUSAGE
undef(my @top_featrels);
undef (my %srcfhash);
- local($^W) = 0; # supressing warnings about uninitialized fields.
+ local($^W) = 0; # suppressing warnings about uninitialized fields.
if (!$name && $seq->can('attributes') ) {
($name) = $seq->attributes('Alias');
diff --git a/Bio/SeqIO/chaos.pm b/Bio/SeqIO/chaos.pm
index 622bafa..ccf1275 100644
--- a/Bio/SeqIO/chaos.pm
+++ b/Bio/SeqIO/chaos.pm
@@ -367,7 +367,7 @@ sub write_seq {
} qw(desc keywords division molecule is_circular);
$prop{dates} = join("; ", $seq->get_dates) if $seq->can("get_dates");
- local($^W) = 0; # supressing warnings about uninitialized fields.
+ local($^W) = 0; # suppressing warnings about uninitialized fields.
# Reference lines
my $count = 1;
diff --git a/Bio/SeqIO/embl.pm b/Bio/SeqIO/embl.pm
index b35b63a..a856c1e 100644
--- a/Bio/SeqIO/embl.pm
+++ b/Bio/SeqIO/embl.pm
@@ -926,7 +926,7 @@ sub write_seq {
Title : _print_EMBL_FTHelper
Usage :
Function: Internal function
- Returns : 1 if writing suceeded, otherwise undef
+ Returns : 1 if writing succeeded, otherwise undef
Args :
@@ -953,7 +953,7 @@ sub _print_EMBL_FTHelper {
$self->_write_line_EMBL_regex(sprintf("FT %-15s ",$fth->key),
"FT ",$fth->loc,
'\,|$',80) || return; #'
- foreach my $tag ( keys %{$fth->field} ) {
+ foreach my $tag (sort keys %{$fth->field} ) {
if ( ! defined $fth->field->{$tag} ) {
next;
}
@@ -1433,7 +1433,7 @@ sub _read_FTHelper_EMBL {
Usage :
Function: internal function
Example :
- Returns : 1 if writing suceeded, else undef
+ Returns : 1 if writing succeeded, else undef
Args :
diff --git a/Bio/SeqIO/fasta.pm b/Bio/SeqIO/fasta.pm
index 8b693d2..fe58ae6 100644
--- a/Bio/SeqIO/fasta.pm
+++ b/Bio/SeqIO/fasta.pm
@@ -300,7 +300,7 @@ sub width {
Usage : $obj->block($newval)
Function: Get/Set the length of each block for FASTA output. Sequence blocks
will be split with a space. Configuring block, to a value of 10 for
- example, allows to easily indentify a position in a sequence by eye.
+ example, allows one to easily identify a position in a sequence by eye.
Default : same value used for width.
Returns : value of block
Args : newvalue (optional)
diff --git a/Bio/SeqIO/fastq.pm b/Bio/SeqIO/fastq.pm
index c20f5d0..f17d4e0 100644
--- a/Bio/SeqIO/fastq.pm
+++ b/Bio/SeqIO/fastq.pm
@@ -475,7 +475,7 @@ methods. Internal methods are usually preceded with a _
quality data.
Current values accepted are:
- 'sanger' (orginal FASTQ)
+ 'sanger' (original FASTQ)
ASCII encoding from 33-126, PHRED quality score from 0 to 93
'solexa' (aka illumina1.0)
ASCII encoding from 59-104, SOLEXA quality score from -5 to 40
diff --git a/Bio/SeqIO/game/gameHandler.pm b/Bio/SeqIO/game/gameHandler.pm
index 05c5db4..559c5ca 100644
--- a/Bio/SeqIO/game/gameHandler.pm
+++ b/Bio/SeqIO/game/gameHandler.pm
@@ -114,7 +114,7 @@ sub end_document {
Usage : $seqs = $handler->load
Function: start parsing
Returns : a ref to a list of sequence objects
- Args : an optional flag to supress <computation_analysis> elements (not used yet)
+ Args : an optional flag to suppress <computation_analysis> elements (not used yet)
=cut
diff --git a/Bio/SeqIO/gcg.pm b/Bio/SeqIO/gcg.pm
index f384540..c95059a 100644
--- a/Bio/SeqIO/gcg.pm
+++ b/Bio/SeqIO/gcg.pm
@@ -273,10 +273,10 @@ sub GCG_checksum {
Function: if parsed gcg sequence contains a checksum field
: we compare it to a value computed here on the parsed
: sequence. A checksum mismatch would indicate some
- : type of parsing failure occured.
+ : type of parsing failure occurred.
:
Returns : 1 for success, 0 for failure
- Args : string containing parsed seq, value of parsed cheksum
+ Args : string containing parsed seq, value of parsed checksum
=cut
diff --git a/Bio/SeqIO/genbank.pm b/Bio/SeqIO/genbank.pm
index 7e28e94..6bc8f37 100644
--- a/Bio/SeqIO/genbank.pm
+++ b/Bio/SeqIO/genbank.pm
@@ -89,7 +89,7 @@ associated Bio::AnnotationCollectionI object which is associated with
Bio::Seq objects. If it is explicitly requested that no annotations
should be stored when parsing a record of course they will not be
available when you try and get them. If you are having this problem
-look at the type of SeqBuilder that is being used to contruct your
+look at the type of SeqBuilder that is being used to construct your
sequence object.
Comments Annotation 'comment'
@@ -117,7 +117,7 @@ sequence object.
There is more information in the Feature-Annotation HOWTO about each
field and how it is mapped to the Sequence object
-L<http://bioperl.open-bio.org/wiki/HOWTO:Feature-Annotation>.
+L<http://bioperl.org/howtos/Features_and_Annotations_HOWTO.html>.
=head1 FEEDBACK
@@ -500,7 +500,7 @@ sub next_seq {
}
# Comments may be plain text or Structured Comments.
- # Structured Comments are made up of tag/value pairs and have beginning
+ # Structured Comments are made up of tag/value pairs and have beginning
# and end delimiters like ##*-Data-START## and ##*-Data-END##
elsif ($line =~ /^COMMENT\s+(\S.*)/) {
if ($annotation) {
@@ -965,7 +965,7 @@ sub write_seq {
my $circular = ($seq->is_circular) ? 'circular' : 'linear ';
- local($^W) = 0; # supressing warnings about uninitialized fields.
+ local($^W) = 0; # suppressing warnings about uninitialized fields.
my $temp_line;
if ( $self->_id_generation_func ) {
@@ -1273,7 +1273,7 @@ sub _print_GenBank_FTHelper {
sprintf( " %-16s%s", $fth->key, $spacer ),
" " x 21, $fth->loc, "\,\|\$", 80 );
- foreach my $tag ( keys %{ $fth->field } ) {
+ foreach my $tag ( sort keys %{ $fth->field } ) {
# Account for hash structure in Annotation::DBLink, not the expected array
if ( $tag eq 'db_xref' and grep /HASH/, @{ $fth->field->{$tag} }) {
for my $ref ( @{ $fth->field->{$tag} } ) {
@@ -1330,7 +1330,7 @@ sub _read_GenBank_References {
my (@refs);
my $ref;
- # assumme things are starting with RN
+ # assume things are starting with RN
if ( $$buffer !~ /^REFERENCE/ ) {
warn("Not parsing line '$$buffer' which maybe important");
}
diff --git a/Bio/SeqIO/interpro.pm b/Bio/SeqIO/interpro.pm
index 30138db..cef7608 100644
--- a/Bio/SeqIO/interpro.pm
+++ b/Bio/SeqIO/interpro.pm
@@ -120,7 +120,7 @@ sub next_seq {
my $wingwhere = index($line, $wing);
# the interpro XML is not fully formed, so we need to convert the
- # extra double quotes and ampersands into appropriate XML chracter codes
+ # extra double quotes and ampersands into appropriate XML character codes
if($where > 0){
my @linearray = split /$zinc/, $line;
$finishedline = join ""zincins"", $linearray[0], $linearray[2];
diff --git a/Bio/SeqIO/lasergene.pm b/Bio/SeqIO/lasergene.pm
index 1d3f0dc..bc2513b 100644
--- a/Bio/SeqIO/lasergene.pm
+++ b/Bio/SeqIO/lasergene.pm
@@ -25,7 +25,7 @@ Do not use this module directly. Use it via the L<Bio::SeqIO> class.
This object can product Bio::Seq::RichSeq objects from Lasergene sequence files.
-IT DOES NOT PARSE ANY ATTIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE.
+IT DOES NOT PARSE ANY ATTRIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE.
IT DOES NOT WRITE THESE FILES EITHER.
diff --git a/Bio/SeqIO/mbsout.pm b/Bio/SeqIO/mbsout.pm
index 6859055..41b867c 100644
--- a/Bio/SeqIO/mbsout.pm
+++ b/Bio/SeqIO/mbsout.pm
@@ -653,7 +653,7 @@ Function: returns a reference to a hash. The keys of the hash are the letters
Bio::SeqIO::mbsout stream should be translated to.
Returns : reference to a hash
Args : NONE
-Synopsys:
+Synopsis:
# retrieve the Bio::Seq object's sequence
my $haplotype = $seq->seq;
diff --git a/Bio/SeqIO/msout.pm b/Bio/SeqIO/msout.pm
index 2856860..8e8e58e 100644
--- a/Bio/SeqIO/msout.pm
+++ b/Bio/SeqIO/msout.pm
@@ -757,7 +757,7 @@ Function: returns a reference to a hash. The keys of the hash are the letters '
Bio::SeqIO::msout stream should be translated to.
Returns : reference to a hash
Args : NONE
-Synopsys:
+Synopsis:
# retrieve the Bio::Seq object's sequence
my $haplotype = $seq->seq;
diff --git a/Bio/SeqIO/pir.pm b/Bio/SeqIO/pir.pm
index 63a06a9..89b5780 100644
--- a/Bio/SeqIO/pir.pm
+++ b/Bio/SeqIO/pir.pm
@@ -1,9 +1,7 @@
#
# BioPerl module for Bio::SeqIO::PIR
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
-#
-# Cared for by Aaron Mackey <amackey at virginia.edu>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Copyright Aaron Mackey
#
@@ -43,15 +41,15 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -110,21 +108,23 @@ sub next_seq {
my ($self) = @_;
local $/ = "\n>";
return unless my $line = $self->_readline;
- if( $line eq '>' ) { # handle the very first one having no comment
- return unless $line = $self->_readline;
+ if ( $line eq '>' ) { # handle the very first one having no comment
+ return unless $line = $self->_readline;
+ }
+ my ( $top, $desc, $seq ) = ( $line =~ /^(.+?)\n(.*?)\n([^>]*)/s )
+ or $self->throw("Cannot parse entry PIR entry [$line]");
+
+ my ( $type, $id );
+ if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) {
+ ( $type, $id ) = ( $1, $2 );
+ if ( ! exists $VALID_TYPE{$type} ) {
+ $self->throw(
+ "PIR stream read attempted without proper two-letter sequence code [ $type ]"
+ );
+ }
+ } else {
+ $self->throw("Line does not match PIR format [ $line ]");
}
- my ($top, $desc,$seq) = ( $line =~ /^(.+?)\n(.+?)\n([^>]*)/s ) or
- $self->throw("Cannot parse entry PIR entry [$line]");
-
- my ( $type,$id );
- if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) {
- ( $type,$id ) = ($1, $2);
- if (!exists $VALID_TYPE{$type} ) {
- $self->throw("PIR stream read attempted without proper two-letter sequence code [ $type ]");
- }
- } else {
- $self->throw("Line does not match PIR format [ $line ]");
- }
# P - indicates complete protein
# F - indicates protein fragment
@@ -132,17 +132,18 @@ sub next_seq {
# suitable for writing out.
$seq =~ s/\*//g;
$seq =~ s/[\(\)\.\/\=\,]//g;
- $seq =~ s/\s+//g; # get rid of whitespace
+ $seq =~ s/\s+//g; # get rid of whitespace
my ($alphabet) = ('protein');
+
# TODO - not processing SFS data
- return $self->sequence_factory->create
- (-seq => $seq,
- -primary_id => $id,
- -id => $id,
- -desc => $desc,
- -alphabet => $alphabet
- );
+ return $self->sequence_factory->create(
+ -seq => $seq,
+ -primary_id => $id,
+ -id => $id,
+ -desc => $desc,
+ -alphabet => $alphabet
+ );
}
=head2 write_seq
diff --git a/Bio/SeqIO/seqxml.pm b/Bio/SeqIO/seqxml.pm
index c6cee85..79a9e58 100644
--- a/Bio/SeqIO/seqxml.pm
+++ b/Bio/SeqIO/seqxml.pm
@@ -906,7 +906,7 @@ sub element_property {
push @{ $data->{'properties'} }, $annotation_obj;
}
else {
- $self->throw("malformated property!");
+ $self->throw("malformatted property!");
}
}
diff --git a/Bio/SeqIO/swiss.pm b/Bio/SeqIO/swiss.pm
index 3e2648a..8978f7c 100644
--- a/Bio/SeqIO/swiss.pm
+++ b/Bio/SeqIO/swiss.pm
@@ -478,7 +478,7 @@ sub next_seq {
-annotation => $annotation,
);
- # The annotation doesn't get added by the contructor
+ # The annotation doesn't get added by the constructor
$seq->annotation($annotation);
return $seq;
@@ -549,7 +549,7 @@ sub write_seq {
$self->_print( "ID $temp_line\n");
# if there, write the accession line
- local($^W) = 0; # supressing warnings about uninitialized fields
+ local($^W) = 0; # suppressing warnings about uninitialized fields
if ( $self->_ac_generation_func ) {
$temp_line = &{$self->_ac_generation_func}($seq);
diff --git a/Bio/SeqIO/tigr.pm b/Bio/SeqIO/tigr.pm
index fea4d58..8833001 100644
--- a/Bio/SeqIO/tigr.pm
+++ b/Bio/SeqIO/tigr.pm
@@ -263,7 +263,7 @@ sub _process_pseudochromosome
return;
}
- $self->throw("Reached end of _process_psuedochromosome");
+ $self->throw("Reached end of _process_pseudochromosome");
}
sub _process_assembly
@@ -364,7 +364,7 @@ sub _process_assembly_seq()
"with no <ASSEMBLY_SEQUENCE> in the stream");
}
- # Protect agains lots of smaller lines
+ # Protect against lots of smaller lines
my @chunks;
do {
diff --git a/Bio/SeqUtils.pm b/Bio/SeqUtils.pm
index 287fcd8..b2ad21b 100644
--- a/Bio/SeqUtils.pm
+++ b/Bio/SeqUtils.pm
@@ -51,7 +51,7 @@ Bio::SeqUtils - Additional methods for PrimarySeq objects
my $revcomseq = Bio::SeqUtils->revcom_with_features($seq);
# simulate cloning of a fragment into a vector. Cut the vector at
- # positions 1000 and 1100 (deleting postions 1001 to 1099) and
+ # positions 1000 and 1100 (deleting positions 1001 to 1099) and
# "ligate" a fragment into the sites. The fragment is
# reverse-complemented in this example (option "flip").
# All features of the vector and fragment are preserved and
diff --git a/Bio/Structure/Entry.pm b/Bio/Structure/Entry.pm
index c913c81..aed8f92 100644
--- a/Bio/Structure/Entry.pm
+++ b/Bio/Structure/Entry.pm
@@ -212,7 +212,7 @@ sub add_model {
}
push @{$self->{'model'}}, $m;
# create a stringified version of our ref
- # not used untill we get symbolic ref working
+ # not used until we get symbolic ref working
#my $str_ref = "$self";
#$m->_grandparent($str_ref);
}
@@ -798,7 +798,7 @@ sub parent {
$self->throw("parent: you need to supply an argument to get the parent from\n");
}
- # for now we pass on to _parent, untill we get the symbolic ref thing working.
+ # for now we pass on to _parent, until we get the symbolic ref thing working.
$self->_parent($obj);
}
diff --git a/Bio/Structure/Residue.pm b/Bio/Structure/Residue.pm
index 0e23956..a5e189b 100644
--- a/Bio/Structure/Residue.pm
+++ b/Bio/Structure/Residue.pm
@@ -116,7 +116,7 @@ sub new {
Title : atom
Usage :
- Function: nothing useful untill I get symbolic references to do what I want
+ Function: nothing useful until I get symbolic references to do what I want
Returns :
Args :
@@ -133,7 +133,7 @@ sub atom {
Title : add_atom
Usage :
- Function: nothing useful untill I get symbolic references to do what I want
+ Function: nothing useful until I get symbolic references to do what I want
Returns :
Args :
diff --git a/Bio/Structure/SecStr/DSSP/Res.pm b/Bio/Structure/SecStr/DSSP/Res.pm
index 73c9311..15efa7e 100644
--- a/Bio/Structure/SecStr/DSSP/Res.pm
+++ b/Bio/Structure/SecStr/DSSP/Res.pm
@@ -1190,10 +1190,10 @@ sub _toDsspKey {
if ( ! $chain_id) { # parse the lone argument
( $key_num, $chain_id, $ins_code )
- = $key_num =~ m/([0-9]+)
- ([a-zA-z]?)
- (?::([a-zA-Z]))?/xms
- ? ( $1, $2, $3 )
+ = $key_num =~ m/^(\-?[0-9]+) # PDB coords can be negative
+ ([a-zA-Z]?)
+ (?::([a-zA-Z\-]))?$/x # missing chains are '-'
+ ? ( $1, $3, $2 )
: $self->throw("Could not derive PDB key $key_num");
}
diff --git a/Bio/Structure/SecStr/STRIDE/Res.pm b/Bio/Structure/SecStr/STRIDE/Res.pm
index 16e9b93..78aa485 100644
--- a/Bio/Structure/SecStr/STRIDE/Res.pm
+++ b/Bio/Structure/SecStr/STRIDE/Res.pm
@@ -42,7 +42,7 @@ individual residues of a pdb structure file.
STRIDE is available here:
http://webclu.bio.wzw.tum.de/stride/
-Methods are then available for extracting all of the infomation
+Methods are then available for extracting all of the information
present within the output or convenient subsets of it.
Although they are very similar in function, DSSP and STRIDE differ
diff --git a/Bio/Taxonomy.pm b/Bio/Taxonomy.pm
index 90419a1..eba74b9 100644
--- a/Bio/Taxonomy.pm
+++ b/Bio/Taxonomy.pm
@@ -389,7 +389,7 @@ sub add_node {
Title : binomial
Usage : my $val = $obj->binomial;
- Function: returns the binomial name if this taxonomy reachs species level
+ Function: returns the binomial name if this taxonomy reaches species level
Returns : the binomial name
OR undef if taxonmy does not reach species level
Args : [No arguments]
@@ -410,7 +410,7 @@ sub binomial {
Usage : $node = $taxonomy->get_node('species');
Function: get a Bio::Taxonomy::Node object according to rank name
Returns : a Bio::Taxonomy::Node object or undef if null
- Args : a vaild rank name
+ Args : a valid rank name
=cut
diff --git a/Bio/Tools/AlignFactory.pm b/Bio/Tools/AlignFactory.pm
index 03b87d8..54f0c9d 100644
--- a/Bio/Tools/AlignFactory.pm
+++ b/Bio/Tools/AlignFactory.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::Tools::AlignFactory
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by Ewan Birney <birney at sanger.ac.uk>
#
@@ -17,7 +17,7 @@ Bio::Tools::AlignFactory - Base object for alignment factories
=head1 SYNOPSIS
-You wont be using this as an object, but using a dervied class
+You won't be using this as an object, but using a dervied class
like Bio::Tools::pSW
=head1 DESCRIPTION
@@ -26,7 +26,7 @@ Holds common Alignment Factory attributes in place
=head1 CONTACT
-http://bio.perl.org/ or birney at sanger.ac.uk
+http://bio.perl.org/ or birney at sanger.ac.uk
=head1 APPENDIX
@@ -58,9 +58,9 @@ sub new {
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
# set up defaults
-
+
$self->{'kbyte'} = 20000;
- $self->{'report'} = 0;
+ $self->{'report'} = 0;
return $self;
}
@@ -69,20 +69,20 @@ sub new {
Title : kbyte()
Usage : set/gets the amount of memory able to be used
- Function :
+ Function :
: $factory->kbyte(200);
:
- Returns :
+ Returns :
Argument : memory in kilobytes
=cut
sub kbyte {
my ($self,$value) = @_;
-
+
if( defined $value ) {
$self->{'kbyte'} = $value;
- }
+ }
return $self->{'kbyte'};
}
@@ -91,7 +91,7 @@ sub kbyte {
Title : report()
Usage : set/gets the report boolean to issue reports or not
- Function :
+ Function :
: $factory->report(1); # reporting goes on
:
Returns : n/a
@@ -101,14 +101,14 @@ sub kbyte {
sub report {
my ($self,$value) = @_;
-
+
if( defined $value ) {
if( $value != 1 && $value != 0 ) {
$self->throw("Attempting to modify AlignFactory Report with no boolean value!");
}
$self->{'report'} = $value;
- }
+ }
return $self->{'report'};
}
@@ -119,7 +119,7 @@ sub report {
Usage : Only used by subclasses.
Function:
Example :
- Returns :
+ Returns :
Args :
diff --git a/Bio/Tools/Analysis/DNA/ESEfinder.pm b/Bio/Tools/Analysis/DNA/ESEfinder.pm
index 69cece2..abfeb8d 100644
--- a/Bio/Tools/Analysis/DNA/ESEfinder.pm
+++ b/Bio/Tools/Analysis/DNA/ESEfinder.pm
@@ -86,7 +86,7 @@ score]
See L<http://rulai.cshl.edu/tools/ESE2/>
-This the second implentation of Bio::SimpleAnalysisI which hopefully
+This the second implementation of Bio::SimpleAnalysisI which hopefully
will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from L<Bio::WebAgent>.
diff --git a/Bio/Tools/Analysis/Protein/ELM.pm b/Bio/Tools/Analysis/Protein/ELM.pm
index 508af00..ef71958 100755
--- a/Bio/Tools/Analysis/Protein/ELM.pm
+++ b/Bio/Tools/Analysis/Protein/ELM.pm
@@ -205,7 +205,7 @@ sub compartment {
name : species
usage : $tool->species('9606');
- purpose : get/setter for species selction for ELM server
+ purpose : get/setter for species selection for ELM server
arguments : none, taxon_id or Bio::Species object
returns : a string of the ncbi taxon_id
diff --git a/Bio/Tools/Analysis/Protein/NetPhos.pm b/Bio/Tools/Analysis/Protein/NetPhos.pm
index 06faad0..81543d7 100644
--- a/Bio/Tools/Analysis/Protein/NetPhos.pm
+++ b/Bio/Tools/Analysis/Protein/NetPhos.pm
@@ -54,7 +54,7 @@ phosphorylation sites in eukaryotic proteins.
See L<http://www.cbs.dtu.dk/services/NetPhos/>.
-This the first implentation of Bio::SimpleAnalysisI which hopefully
+This the first implementation of Bio::SimpleAnalysisI which hopefully
will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from Bio::WebAgent.
@@ -233,7 +233,7 @@ sub result {
Usage : $job->threshold(...)
Returns : The significance threshold of a prediction
- Args : None (retrieves value) or a value beween 0 and 1.
+ Args : None (retrieves value) or a value between 0 and 1.
Purpose : Get/setter of the threshold to be sumitted for analysis.
=cut
diff --git a/Bio/Tools/ECnumber.pm b/Bio/Tools/ECnumber.pm
index ad198e7..ae918c3 100644
--- a/Bio/Tools/ECnumber.pm
+++ b/Bio/Tools/ECnumber.pm
@@ -69,7 +69,7 @@ Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
=head1 DESCRIPTION
L<Bio::Tools::ECnumber> is a representation of EC numbers,
-the numerical heirarchy for Enzyme Classification.
+the numerical hierarchy for Enzyme Classification.
See L<http://www.chem.qmul.ac.uk/iubmb/enzyme/> for more details.
diff --git a/Bio/Tools/GFF.pm b/Bio/Tools/GFF.pm
index 8067bac..f8cc068 100644
--- a/Bio/Tools/GFF.pm
+++ b/Bio/Tools/GFF.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::Tools::GFF
#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
#
# Cared for by the Bioperl core team
#
@@ -105,15 +105,15 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l at bioperl.org>
-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
+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
@@ -127,7 +127,7 @@ the bugs and their resolution. Bug reports can be submitted the web:
Email mrp-at-sanger.ac.uk
-=head1 CONTRIBUTORS
+=head1 CONTRIBUTORS
Jason Stajich, jason-at-biperl-dot-org
Chris Mungall, cjm-at-fruitfly-dot-org
@@ -180,9 +180,9 @@ my %SKIPPED_TAGS = map { $_ => 1 } qw(score);
{ # make a class variable such that we can generate unique ID's over
# a session, no matter how many instances of GFF.pm we make
# since these have to be unique within the scope of a GFF file.
-
+
my $gff3_featureID = 0;
-
+
sub _incrementGFF3ID {
my ($self) = @_;
return ++ $gff3_featureID;
@@ -193,7 +193,7 @@ my %SKIPPED_TAGS = map { $_ => 1 } qw(score);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
-
+
my ($gff_version, $noparse) = $self->_rearrange([qw(GFF_VERSION NOPARSE)], at args);
# initialize IO
@@ -261,7 +261,7 @@ sub _parse_header{
$self->throw("##FASTA directive must be followed by fasta header, not: $line");
}
}
-
+
if ($line =~ /^\>(.*)/) {
# seq data can be at header or footer
my $seq = $self->_parse_sequence($line);
@@ -269,7 +269,7 @@ sub _parse_header{
$self->_seq_by_id_h->{$seq->primary_id} = $seq;
}
}
-
+
if(!$handled){
push @unhandled, $line;
@@ -290,7 +290,7 @@ sub _parse_sequence {
my ($self, $line) = @_;
if ($line =~ /^\>(.*)/) {
-
+
my $seqid = $1;
$seqid =~ s/\s+$//;
my $desc = '';
@@ -312,12 +312,12 @@ sub _parse_sequence {
return if $self->ignore_sequence;
my $seqfactory = Bio::Seq::SeqFactory->new('Bio::Seq');
- my $seq = $seqfactory->create(-seq=>$res,
+ my $seq = $seqfactory->create(-seq=>$res,
-id=>$seqid,
-desc=>$desc);
$seq->accession_number($seqid);
if ($self->features_attached_to_seqs) {
- my @feats =
+ my @feats =
@{$self->_feature_idx_by_seq_id->{$seqid}};
$seq->add_SeqFeature($_) foreach @feats;
@{$self->_feature_idx_by_seq_id->{$seqid}} = ();
@@ -334,7 +334,7 @@ sub _parse_sequence {
Title : next_segment
Usage : my $seq = $gffio->next_segment;
- Function: Returns a Bio::LocatableSeq object corresponding to a
+ Function: Returns a Bio::LocatableSeq object corresponding to a
GFF "##sequence-region" header line.
Example :
Returns : A Bio::LocatableSeq object, or undef if
@@ -360,15 +360,15 @@ sub next_segment{
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
- Args : none
+ Args : none
=cut
sub next_feature {
my ($self) = @_;
-
+
my $gff_string;
-
+
# be graceful about empty lines or comments, and make sure we return undef
# if the input's consumed
while(($gff_string = $self->_readline()) && defined($gff_string)) {
@@ -387,7 +387,7 @@ sub next_feature {
last unless $gff_string;
}
}
- last;
+ last;
}
return unless $gff_string;
@@ -456,7 +456,7 @@ sub from_gff_string {
sub _from_gff1_string {
my ($gff, $feat, $string) = @_;
chomp $string;
- my ($seqname, $source, $primary, $start, $end, $score,
+ my ($seqname, $source, $primary, $start, $end, $score,
$strand, $frame, @group) = split(/\t/, $string);
if ( !defined $frame ) {
@@ -511,15 +511,15 @@ sub _from_gff2_string {
# text-translated tab symbols but no "real" tabs, so splitting on
# \t is safe, and $attribs gets the entire attributes field to be
# parsed later
-
+
# sendu: but the tag value pair can (should?) be separated by a tab. The
# 'no tabs' thing seems to apply only to the free text that is allowed for
# the value
- my ($seqname, $source, $primary, $start,
+ my ($seqname, $source, $primary, $start,
$end, $score, $strand, $frame, @attribs) = split(/\t+/, $string);
my $attribs = join ' ', @attribs;
-
+
if ( !defined $frame ) {
$feat->throw("[$string] does not look like GFF2 to me");
}
@@ -539,40 +539,40 @@ sub _from_gff2_string {
if ( $strand eq '.' ) { $feat->strand(0); }
- # <Begin Inefficient Code from Mark Wilkinson>
+ # <Begin Inefficient Code from Mark Wilkinson>
# this routine is necessay to allow the presence of semicolons in
# quoted text Semicolons are the delimiting character for new
# tag/value attributes. it is more or less a "state" machine, with
# the "quoted" flag going up and down as we pass thorugh quotes to
# distinguish free-text semicolon and hash symbols from GFF control
# characters
-
+
my $flag = 0; # this could be changed to a bit and just be twiddled
my @parsed;
# run through each character one at a time and check it
# NOTE: changed to foreach loop which is more efficient in perl
# --jasons
- for my $a ( split //, $attribs ) {
+ for my $a ( split //, $attribs ) {
# flag up on entering quoted text, down on leaving it
if( $a eq '"') { $flag = ( $flag == 0 ) ? 1:0 }
elsif( $a eq ';' && $flag ) { $a = "INSERT_SEMICOLON_HERE"}
- elsif( $a eq '#' && ! $flag ) { last }
+ elsif( $a eq '#' && ! $flag ) { last }
push @parsed, $a;
}
$attribs = join "", @parsed; # rejoin into a single string
- # <End Inefficient Code>
+ # <End Inefficient Code>
# Please feel free to fix this and make it more "perlish"
my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited
foreach my $pair ( @key_vals ) {
# replace semicolons that were removed from free-text above.
- $pair =~ s/INSERT_SEMICOLON_HERE/;/g;
+ $pair =~ s/INSERT_SEMICOLON_HERE/;/g;
# separate the key from the value
- my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair;
+ my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair;
if( defined $values ) {
my @values;
@@ -580,18 +580,18 @@ sub _from_gff2_string {
# and remove it from the $values string
while ($values =~ s/"(.*?)"//){
# and push it on to the list of values (tags may have
- # more than one value... and the value may be undef)
+ # more than one value... and the value may be undef)
push @values, $1;
}
# and what is left over should be space-separated
# non-free-text values
- my @othervals = split /\s+/, $values;
+ my @othervals = split /\s+/, $values;
foreach my $othervalue(@othervals){
- # get rid of any empty strings which might
+ # get rid of any empty strings which might
# result from the split
- if (CORE::length($othervalue) > 0) {push @values, $othervalue}
+ if (CORE::length($othervalue) > 0) {push @values, $othervalue}
}
foreach my $value(@values){
@@ -606,13 +606,13 @@ sub _from_gff3_string {
my ($gff, $feat, $string) = @_;
chomp($string);
- # according to the now nearly final GFF3 spec, columns should
+ # according to the now nearly final GFF3 spec, columns should
# be tab separated, allowing unescaped spaces to occur in
# column 9
- my ($seqname, $source, $primary, $start, $end,
+ my ($seqname, $source, $primary, $start, $end,
$score, $strand, $frame, $groups) = split(/\t/, $string);
-
+
if ( ! defined $frame ) {
$feat->throw("[$string] does not look like GFF3 to me");
}
@@ -706,7 +706,7 @@ sub gff_string{
Title : _gff1_string
Usage : $gffstr = $gffio->_gff1_string
- Function:
+ Function:
Example :
Returns : A GFF1-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF-stringified
@@ -735,7 +735,7 @@ sub _gff1_string{
} elsif ( $feat->strand == -1 ) {
$strand = '-';
}
-
+
if( $feat->can('seqname') ) {
$name = $feat->seq_id();
$name ||= 'SEQ';
@@ -768,7 +768,7 @@ sub _gff1_string{
Title : _gff2_string
Usage : $gffstr = $gffio->_gff2_string
- Function:
+ Function:
Example :
Returns : A GFF2-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified
@@ -827,7 +827,7 @@ sub _gff2_string{
# standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values
# must be quoted with double quotes".
# MW
-
+
my @group;
foreach my $tag ( $feat->get_all_tags ) {
@@ -855,11 +855,11 @@ sub _gff2_string{
! $feat->has_tag('Group') &&
$origfeat->isa('Bio::SeqFeature::FeaturePair') ) {
$str2 = sprintf("Target %s %d %d", $origfeat->feature1->seq_id,
- ( $origfeat->feature1->strand < 0 ?
+ ( $origfeat->feature1->strand < 0 ?
( $origfeat->feature1->end,
$origfeat->feature1->start) :
( $origfeat->feature1->start,
- $origfeat->feature1->end)
+ $origfeat->feature1->end)
)) . ($str2?" ; ".$str2:""); # need to put Target information before other tag/value pairs - mw
}
return $str1."\t".$str2;
@@ -932,18 +932,18 @@ sub _gff25_string {
unless( defined $value && length($value) ) {
$value = '""';
} elsif ($value =~ /[^A-Za-z0-9_]/){
- $value =~ s/\t/\\t/g; # substitute tab and newline
+ $value =~ s/\t/\\t/g; # substitute tab and newline
# characters
$value =~ s/\n/\\n/g; # to their UNIX equivalents
$value = '"' . $value . '" ';
- } # if the value contains
- # anything other than valid
- # tag/value characters, then
+ } # if the value contains
+ # anything other than valid
+ # tag/value characters, then
# quote it
push @v, $value;
# for this tag (allowed in GFF2 and .ace format)
}
- if (($tag eq 'Group') || ($tag eq 'Target')){ # hopefully we wont get both...
+ if (($tag eq 'Group') || ($tag eq 'Target')){ # hopefully we won't get both...
push @firstgroup, "$tag ".join(" ", @v);
} else {
push @group, "$tag ".join(" ", @v);
@@ -956,11 +956,11 @@ sub _gff25_string {
! $feat->has_tag('Group') &&
$origfeat->isa('Bio::SeqFeature::FeaturePair') ) {
$str2 = sprintf("Target %s ; tstart %d ; tend %d", $origfeat->feature1->seq_id,
- ( $origfeat->feature1->strand < 0 ?
+ ( $origfeat->feature1->strand < 0 ?
( $origfeat->feature1->end,
$origfeat->feature1->start) :
( $origfeat->feature1->start,
- $origfeat->feature1->end)
+ $origfeat->feature1->end)
)) . ($str2?" ; ".$str2:""); # need to put the target info before other tag/value pairs - mw
}
return $str1 . "\t". $str2;
@@ -971,7 +971,7 @@ sub _gff25_string {
Title : _gff3_string
Usage : $gffstr = $gffio->_gff3_string
- Function:
+ Function:
Example :
Returns : A GFF3-formatted string representation of the SeqFeature
Args : A Bio::SeqFeatureI implementing object to be GFF3-stringified
@@ -1030,34 +1030,34 @@ sub _gff3_string {
for my $tag ( @all_tags ) {
next if exists $SKIPPED_TAGS{$tag};
# next if $tag eq 'Target';
- if ($tag eq 'Target' && ! $origfeat->isa('Bio::SeqFeature::FeaturePair')){
+ if ($tag eq 'Target' && ! $origfeat->isa('Bio::SeqFeature::FeaturePair')){
my @values = $feat->get_tag_values($tag);
if(scalar(@values) > 1){ # How is it possible that Target is has a value list ??
# simple Target,start,stop
- my ($target_id, $b,$e,$strand) = $feat->get_tag_values($tag);
+ my ($target_id, $b,$e,$strand) = $feat->get_tag_values($tag);
next unless(defined($e) && defined($b) && $target_id);
($b,$e)= ($e,$b) if(defined $strand && $strand<0);
#if we have the strand we will print it
if($strand){ push @groups, sprintf("Target=%s %d %d %s", $target_id,$b,$e,$strand); }
else{ push @groups, sprintf("Target=%s %d %d", $target_id,$b,$e); }
next;
- }
+ }
}
my $valuestr;
- # a string which will hold one or more values
- # for this tag, with quoted free text and
+ # a string which will hold one or more values
+ # for this tag, with quoted free text and
# space-separated individual values.
my @v;
for my $value ( $feat->get_tag_values($tag) ) {
- if( defined $value && length($value) ) {
+ if( defined $value && length($value) ) {
#$value =~ tr/ /+/; #spaces are allowed now
if ( ref $value eq 'Bio::Annotation::Comment') {
$value = $value->text;
}
if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) {
- $value =~ s/\t/\\t/g; # substitute tab and newline
+ $value =~ s/\t/\\t/g; # substitute tab and newline
# characters
$value =~ s/\n/\\n/g; # to their UNIX equivalents
@@ -1078,20 +1078,20 @@ sub _gff3_string {
push @groups, "$tag=".join(",", at v);
}
# Add Target information for Feature Pairs
- if( $feat->has_tag('Target') &&
+ if( $feat->has_tag('Target') &&
! $feat->has_tag('Group') &&
$origfeat->isa('Bio::SeqFeature::FeaturePair') ) {
my $target_id = $origfeat->feature1->seq_id;
- $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge;
+ $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge;
- push @groups, sprintf("Target=%s %d %d",
+ push @groups, sprintf("Target=%s %d %d",
$target_id,
- ( $origfeat->feature1->strand < 0 ?
+ ( $origfeat->feature1->strand < 0 ?
( $origfeat->feature1->end,
$origfeat->feature1->start) :
( $origfeat->feature1->start,
- $origfeat->feature1->end)
+ $origfeat->feature1->end)
));
}
@@ -1127,7 +1127,7 @@ sub _gff3_string {
$feat->end(),
$score,
$strand,
- $frame,
+ $frame,
join(';', @groups));
}
return $gff_string;
@@ -1138,7 +1138,7 @@ sub _gff3_string {
Title : _gff_version
Usage : $gffversion = $gffio->gff_version
- Function:
+ Function:
Example :
Returns : The GFF version this parser will accept and emit.
Args : none
@@ -1221,7 +1221,7 @@ sub _seq_by_id_h {
Usage :
Function: Returns all Bio::Seq objects populated by GFF3 file
Example :
- Returns :
+ Returns :
Args :
=cut
@@ -1236,7 +1236,7 @@ sub get_seqs {
Title : features_attached_to_seqs
Usage : $obj->features_attached_to_seqs(1);
- Function: For use with GFF3 containg sequence only
+ Function: For use with GFF3 containing sequence only
Setting this B<before> parsing ensures that all Bio::Seq object
created will have the appropriate features added to them
@@ -1246,7 +1246,7 @@ sub get_seqs {
Note that this mode will incur higher memory usage because features
will have to be cached until the relevant feature comes along
- Example :
+ Example :
Returns : value of features_attached_to_seqs (a boolean)
Args : on set, new value (a boolean, optional)
@@ -1265,12 +1265,12 @@ sub features_attached_to_seqs{
Title : ignore_sequence
Usage : $obj->ignore_sequence(1);
- Function: For use with GFF3 containg sequence only
+ Function: For use with GFF3 containing sequence only
Setting this B<before> parsing means that all sequence data will be
ignored
- Example :
+ Example :
Returns : value of ignore_sequence (a boolean)
Args : on set, new value (a boolean, optional)
diff --git a/Bio/Tools/Phylo/Gerp.pm b/Bio/Tools/Phylo/Gerp.pm
index b81261c..7dba257 100755
--- a/Bio/Tools/Phylo/Gerp.pm
+++ b/Bio/Tools/Phylo/Gerp.pm
@@ -149,7 +149,7 @@ sub next_result {
-end => $end,
-strand => 1,
-score => $rs_score,
- #-type => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirments!
+ #-type => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirements!
-source => 'GERP');
my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
diff --git a/Bio/Tools/Phylo/PAML.pm b/Bio/Tools/Phylo/PAML.pm
deleted file mode 100644
index 32d7f6b..0000000
--- 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 <bioperl-l at bioperl.org>
-#
-# Cared for by Jason Stajich <jason-at-bioperl.org>
-#
-# 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 at 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<bioperl-l at bioperl.org>
-
-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 at sendu.me.uk
-Dave Messina dmessina at 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 ac2e021..0000000
--- 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 <jason at bioperl.org>
-#
-# 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 at 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 at bioperl.org
- http://bioperl.org/bioperl-bugs/
-
-=head1 AUTHOR - Jason Stajich, Aaron Mackey
-
-Email jason at bioperl.org
-Email amackey at 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;
-
- at 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, at 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 = $codemlparser->get_trees();
- Function: Returns a list of trees (if any) are in the output file
- Returns : List of L<Bio::Tree::TreeI> objects
- Args : none
-
-
-=cut
-
-sub get_trees{
- my ($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 1d60a21..0000000
--- 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 <bioperl-l at bioperl.org>
-#
-# Cared for by Jason Stajich <jason at open-bio.org>
-#
-# 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 at 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<bioperl-l at bioperl.org>
-
-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 at 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, at 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, at 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, at args) = @_;
- push @{$self->{'_BEBposselsites'}}, [ @args ];
- return scalar @{$self->{'_BEBposselsites'}};
-}
-
-=head2 next_tree
-
- Title : next_tree
- Usage : my $tree = $factory->next_tree;
- Function: Get the next tree from the factory
- Returns : L<Bio::Tree::TreeI>
- Args : none
-
-=cut
-
-sub next_tree{
- my ($self, at 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<Bio::Tree::TreeI>
-
-=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 fd0fbbd..0000000
--- 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 <bioperl-l at bioperl.org>
-#
-# Cared for by Jason Stajich <jason-at-bioperl.org>
-#
-# 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 at 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<bioperl-l at bioperl.org>
-
-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 $obj = Bio::Tools::Phylo::PAML::Result->new(%data);
- Function: Builds a new Bio::Tools::Phylo::PAML::Result object
- Returns : Bio::Tools::Phylo::PAML::Result
- Args : -trees => array reference of Bio::Tree::TreeI objects
- -MLmatrix => ML matrix
- -seqs => array reference of Bio::PrimarySeqI objects
- -codonpos => array reference of codon positions
- -codonfreq => array reference of codon frequencies
- -version => version string
- -model => model string
- -patterns => hashref with the fields '-patterns', '-ns', '-ls'
- -stats => array ref of misc stats (optional)
- -aafreq => Hashref of AA frequencies (only for AAML)
- -aadistmat => Bio::Matrix::PhylipDist (only for AAML)
- -aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML)
- -ntfreq => array ref of NT frequencies (only for BASEML)
- -seqfile => seqfile used
- -kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML)
- -alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML)
- -NSSitesresult => arrayref of PAML::ModelResult
- -input_params => input params from .ctl file
- -rst => array reference of Bio::PrimarySeqI objects
- of ancestral state reconstruction
- -rst_persite=> arrayref of persite data, this is a complicated set of AoH
- -rst_trees => rst trees with changes coded on the tree
-
-See Also: L<Bio::Tree::TreeI>, L<Bio::PrimarySeqI>, L<Bio::Matrix::PhylipDist>, L<Bio::Tools::Phylo::PAML>
-
-
-=cut
-
-sub new {
- my($class, at 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 = $factory->next_tree;
- Function: Get the next tree from the factory
- Returns : L<Bio::Tree::TreeI>
- Args : none
-
-=cut
-
-sub next_tree{
- my ($self, at 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<Bio::Tree::TreeI>
-
-=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, at 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, at 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<Bio::PrimarySeqI>
-
-=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 = $result->get_seqs
- Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit)
- Returns : Array of Bio::PrimarySeq
- Args : None
-See also : L<Bio::PrimarySeq>
-
-=cut
-
-sub get_seqs{
- my ($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, at 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 Relavent 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<Bio::PrimarySeqI>
-
-=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 = $result->get_rst_seqs
- Function: Get the seqs Bio::PrimarySeq
- Returns : Array of Bio::PrimarySeqI objects
- Args : None
-See also : L<Bio::PrimarySeq>
-
-=cut
-
-sub get_rst_seqs{
- my ($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<Bio::Tree::TreeI>
-
-=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 = $result->get_rst_trees
- Function: Get the trees Bio::Tree::TreeI
- Returns : Array of Bio::Tree::TreeI objects
- Args : None
-See also : L<Bio::Tree::TreeI>
-
-=cut
-
-sub get_rst_trees{
- my ($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/Bio/Tools/PrositeScan.pm b/Bio/Tools/PrositeScan.pm
index 1658aea..ad9d5b9 100644
--- a/Bio/Tools/PrositeScan.pm
+++ b/Bio/Tools/PrositeScan.pm
@@ -8,24 +8,47 @@ Bio::Tools::PrositeScan - Parser for ps_scan result
use Bio::Tools::PrositeScan;
my $factory = Bio::Tools::PrositeScan->new(
- -file => 'out.PrositeScan'
+ -file => 'out.PrositeScan',
+ -format => 'fasta'
);
while(my $match = $factory->next_prediction){
- # $match is of Bio::SeqFeature::FeaturePair
- my $q_id = $fatch->feature1->seq_id;
- my $h_id = $fatch->feature2->seq_id;
+ # $match is a Bio::SeqFeature::FeaturePair
+
+ # Sequence ID
+ my $seq_id = $match->seq_id;
+
+ # PROSITE accession number
+ my $psac = $match->hseq_id;
+
+ # Coordinates
+ my @coords = ( $match->start, $match->end );
+
+ # Subsequence
+ my $seq = $match->feature1->seq;
}
=head1 DESCRIPTION
-This is the parser of the output of ps_scan program. It takes either a file
-handler or a file name, and returns a Bio::SeqFeature::FeaturePair object.
+This is a parser of the output of the ps_scan program. It takes either a file
+handle or a file name, and returns a L<Bio::SeqFeature::FeaturePair> object.
+
+Note that the current implementation parses the entire file at once.
=head1 AUTHOR
Juguang Xiao, juguang at tll.org.sg
+=head1 SEE ALSO
+
+=over
+
+=item * L<ps_scan software|ftp://ftp.expasy.org/databases/prosite/ps_scan>
+
+=item * L<PROSITE User Manual|http://prosite.expasy.org/prosuser.html>
+
+=back
+
=cut
# Let the code begin...
@@ -46,6 +69,12 @@ use base qw(Bio::Root::Root Bio::Root::IO);
Usage : Bio::Tools::PrositeScan->new(-file => 'out.PrositeScan');
Bio::Tools::PrositeScan->new(-fh => \*FH);
Returns : L<Bio::Tools::PrositeScan>
+ Args : -format => string representing the format type for the
+ ps_scan output, REQUIRED
+
+The C<-format> argument must currently be set to C<fasta> since this is the
+only parser implemented. This corresponds with using the ps_scan arguments
+C<-o fasta>.
=cut
@@ -72,12 +101,15 @@ sub format {
=head2 next_prediction
Title : new
- Usage :
+ Usage :
while($result = $factory->next_prediction){
;
}
- Returns : a Bio::SeqFeature::FeaturePair object
+ Returns : a Bio::SeqFeature::FeaturePair object where
+ feature1 is the matched subsequence and
+ feature2 is the PROSITE accession number.
+ See <http://prosite.expasy.org/prosuser.html#conv_ac>.
=cut
@@ -153,7 +185,6 @@ sub _parse_fasta {
push @matches, $fp;
}
push @{$self->{_matches}}, @matches;
-
}
sub _attach_seq {
diff --git a/Bio/Tools/SiRNA.pm b/Bio/Tools/SiRNA.pm
index 8c768c4..55df1b9 100644
--- a/Bio/Tools/SiRNA.pm
+++ b/Bio/Tools/SiRNA.pm
@@ -46,7 +46,7 @@ Bio::SeqFeature::SiRNA::Pair contains two subfeatures
oligos. These objects provide accessors for the information on the
individual reagent pairs.
-This verion of Bio::Tools::SiRNA represents a major change in architecture.
+This version of Bio::Tools::SiRNA represents a major change in architecture.
Specific 'rulesets' for siRNA selection as developed by various groups are
implemented as Bio::Tools::SiRNA::Ruleset objects, which inherit from
Bio::Tools::SiRNA. This will make it easier to add new rule sets or modify
diff --git a/Bio/Tools/Sigcleave.pm b/Bio/Tools/Sigcleave.pm
index a3fb8bd..301334c 100644
--- a/Bio/Tools/Sigcleave.pm
+++ b/Bio/Tools/Sigcleave.pm
@@ -92,7 +92,7 @@ In both cases, the "threshold" setting controls the score reporting
level. If no value for threshold is passed in by the user, the code
defaults to a reporting value of 3.5.
-In this implemntation the accessor will never return any
+In this implementation the accessor will never return any
score/position pair which does not meet the threshold limit. This is
the slightly different from the behaviour of the 8.1 EGCG sigcleave
program which will report the highest of the under-threshold results
diff --git a/Bio/Tools/dpAlign.pm b/Bio/Tools/dpAlign.pm
index bed31d6..9216bed 100644
--- a/Bio/Tools/dpAlign.pm
+++ b/Bio/Tools/dpAlign.pm
@@ -104,7 +104,7 @@ sequences overlap each other.
Dynamic Programming was first introduced by Needleman-Wunsch (1970) to
globally align two sequences. The idea of local alignment was later
introduced by Smith-Waterman (1981). Gotoh (1982) improved both
-algorithms by introducing auxillary arrays that reduced the time
+algorithms by introducing auxiliary arrays that reduced the time
complexity of the algorithms to O(m*n). Miller-Myers (1988) exploits
the divide-and-conquer idea introduced by Hirschberg (1975) to solve
the affine gap cost dynamic programming using only linear space. At
diff --git a/Bio/Tools/pSW.pm b/Bio/Tools/pSW.pm
index 4861257..5a80b0a 100644
--- a/Bio/Tools/pSW.pm
+++ b/Bio/Tools/pSW.pm
@@ -254,14 +254,14 @@ sub pairwise_alignment{
if( $alc->alu(0)->text_label eq 'SEQUENCE' ) {
push(@ostr1,$str1[$alc->alu(0)->start+1]);
} else {
- # assumme it is in insert!
+ # assume it is in insert!
push(@ostr1,'-');
}
if( $alc->alu(1)->text_label eq 'SEQUENCE' ) {
push(@ostr2,$str2[$alc->alu(1)->start+1]);
} else {
- # assumme it is in insert!
+ # assume it is in insert!
push(@ostr2,'-');
}
$alctemp = $alc;
diff --git a/Bio/Tree/AlleleNode.pm b/Bio/Tree/AlleleNode.pm
index 706fea2..425da06 100644
--- a/Bio/Tree/AlleleNode.pm
+++ b/Bio/Tree/AlleleNode.pm
@@ -381,7 +381,7 @@ Methods inherited from L<Bio::Tree::Node>.
Function: The human readable identifier for the node
Returns : value of human readable id
Args : newvalue (optional)
- Note : id cannot contain the chracters '();:'
+ Note : id cannot contain the characters '();:'
"A name can be any string of printable characters except blanks,
colons, semicolons, parentheses, and square brackets. Because you may
diff --git a/Bio/Tree/NodeI.pm b/Bio/Tree/NodeI.pm
index 82a9457..0011d3e 100644
--- a/Bio/Tree/NodeI.pm
+++ b/Bio/Tree/NodeI.pm
@@ -64,7 +64,7 @@ length of the branch between the node and its ancestor, thus a root
node in a Tree will not typically have a valid branch length.
Various implementations of NodeI may extend the basic functions and
-allow storing of other information (like attatching a species object
+allow storing of other information (like attaching a species object
or full sequences used to build a tree or alternative sequences). If
you don't know how to extend a Bioperl object please ask, happy to
help, we would also greatly appreciate contributions with improvements
diff --git a/Bio/Tree/TreeFunctionsI.pm b/Bio/Tree/TreeFunctionsI.pm
index 8f4c87b..51508f1 100644
--- a/Bio/Tree/TreeFunctionsI.pm
+++ b/Bio/Tree/TreeFunctionsI.pm
@@ -31,7 +31,7 @@ Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree explorat
=head1 DESCRIPTION
-This interface provides a set of implementated Tree functions which
+This interface provides a set of implemented Tree functions which
only use the defined methods in the TreeI or NodeI interface.
=head1 FEEDBACK
@@ -129,7 +129,7 @@ sub find_node {
}
# could actually do this by testing $rootnode->can($type) but
- # it is possible that a tree is implemeted with different node types
+ # it is possible that a tree is implemented with different node types
# - although it is unlikely that the root node would be richer than the
# leaf nodes. Can't handle NHX tags right now
@@ -542,7 +542,7 @@ sub merge_lineage {
Function: Splices out all nodes in the tree that have an ancestor and only one
descendent.
Returns : n/a
- Args : none for normal behaviour, true to dis-regard the ancestor requirment
+ Args : none for normal behaviour, true to dis-regard the ancestor requirement
and re-root the tree as necessary
For example, if we are the tree $tree:
diff --git a/Bio/TreeIO/nexus.pm b/Bio/TreeIO/nexus.pm
index 6f497fc..9f6f066 100644
--- a/Bio/TreeIO/nexus.pm
+++ b/Bio/TreeIO/nexus.pm
@@ -31,7 +31,7 @@ basically is just a remapping of trees.
The nexus format allows node comments that are placed inside square
brackets. Usually the comments (implemented as tags for nodes) are
-used to give a name for an internal node or record the bootstap value,
+used to give a name for an internal node or record the bootstrap value,
but other uses are possible.
The FigTree program by Andrew Rambaut adds various rendering
diff --git a/Bio/TreeIO/pag.pm b/Bio/TreeIO/pag.pm
index 52ee3f5..ad944f2 100644
--- a/Bio/TreeIO/pag.pm
+++ b/Bio/TreeIO/pag.pm
@@ -255,7 +255,7 @@ sub next_tree{
Title : name_length
Usage : $self->name_length(20);
- Function: set mininum taxon name length
+ Function: set minimum taxon name length
Returns : integer (length of name)
Args : integer
diff --git a/Bio/Variation/AAReverseMutate.pm b/Bio/Variation/AAReverseMutate.pm
index 30e266c..13cf1b7 100644
--- a/Bio/Variation/AAReverseMutate.pm
+++ b/Bio/Variation/AAReverseMutate.pm
@@ -192,7 +192,7 @@ sub aa_mut {
Sets and returns codon_ori triplet. If value is not set,
returns false. The string has to be three characters
- long. The chracter content is not checked.
+ long. The character content is not checked.
Example :
Returns : string
diff --git a/Bio/Variation/VariantI.pm b/Bio/Variation/VariantI.pm
index 0586e00..de8c656 100644
--- a/Bio/Variation/VariantI.pm
+++ b/Bio/Variation/VariantI.pm
@@ -31,7 +31,7 @@ Bio::Variation::RNAChange and Bio::Variation::AAChange use them.
See L<Bio::Variation::DNAMutation>, L<Bio::Variation::RNAChange>,
and L<Bio::Variation::AAChange> for more information.
-These classes store information, heavy computation to detemine allele
+These classes store information, heavy computation to determine allele
sequences is done elsewhere.
The database cross-references are implemented as
@@ -199,10 +199,10 @@ sub each_Allele{
Function:
Returns or sets the boolean value indicating that the
- variant descibed is a canonical mutation with two alleles
+ variant described is a canonical mutation with two alleles
assinged to be the original (wild type) allele and mutated
allele, respectively. If this value is not set, it is
- assumed that the Variant descibes polymorphisms.
+ assumed that the Variant describes polymorphisms.
Returns : a boolean
diff --git a/Changes b/Changes
index 5a6aa44..c74bb33 100644
--- a/Changes
+++ b/Changes
@@ -31,6 +31,27 @@ them separately on CPAN. Modules considered obsolute (relies on a dead web
service or utilizes strict dependencies that are also considered obsolete) will
be removed.
+1.7.2 - "Entebbe"
+
+ [Bugs]
+
+ * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
+ * #245 - Code coverage fixes [zmughal,cjfields]
+ * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
+ * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
+ * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
+ * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
+ * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
+ * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
+ * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
+ * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
+ * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
+ * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
+
+ [Code changes]
+
+ * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
+
1.7.1 - "Election"
[Bugs]
diff --git a/DEPENDENCIES b/DEPENDENCIES
index a74403f..a35a5e1 100644
--- a/DEPENDENCIES
+++ b/DEPENDENCIES
@@ -18,8 +18,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| AcePerl | * Ace - Interface to ACEDB (Popular | None |
-| | Genome DB) | |
+| AcePerl | * Ace - NA | None |
| | * Ace::Sequence::Homol - NA | |
|==============================================================================|
| Used by: |
@@ -32,8 +31,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Algorithm-Munkres | * Algorithm::Munkres - Solution to | None |
-| | classical Assignment Problem | |
+| Algorithm-Munkres | * Algorithm::Munkres - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -42,8 +40,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Archive-Tar | * Archive::Tar - Read, write and | None |
-| | manipulate tar files | |
+| Archive-Tar | * Archive::Tar - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -52,8 +49,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Array-Compare | * Array::Compare - Class to compare | None |
-| | two arrays | |
+| Array-Compare | * Array::Compare - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -62,9 +58,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Bio-ASN1-EntrezGene | * Bio::ASN1::EntrezGene - Parser | None |
-| | for NCBI Entrez Gene (ASN.1- | |
-| | format) | |
+| Bio-ASN1-EntrezGene | * Bio::ASN1::EntrezGene - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -73,18 +67,66 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Compress-Zlib | * Compress::Zlib - Interface to | None |
-| | zlib compression library | |
+| Bio-FeatureIO | * Bio::SeqFeature::Annotated - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::DB::SeqFeature::Store - Compress::Zlib |
+| * Bio::Tools::Phylo::Gumby - Bio::SeqFeature::Annotated |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| Bio-Graphics | * Bio::Graphics::Wiggle::Loader - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::SeqFeature::Store::berkeleydb - Bio::Graphics::Wiggle::Loader |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| Bio-Phylo | * Bio::Phylo - NA | None |
+| | * Bio::Phylo::Factory - NA | |
+| | * Bio::Phylo::Forest::Tree - NA | |
+| | * Bio::Phylo::IO - NA | |
+| | * Bio::Phylo::Matrices - NA | |
+| | * Bio::Phylo::Matrices::Datum - NA | |
+| | * Bio::Phylo::Matrices::Matrix - NA | |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::Nexml::Factory - Bio::Phylo |
+| * Bio::Nexml::Factory - Bio::Phylo::Factory |
+| * Bio::Nexml::Factory - Bio::Phylo::Forest::Tree |
+| * Bio::Nexml::Factory - Bio::Phylo::IO |
+| * Bio::Nexml::Factory - Bio::Phylo::Matrices |
+| * Bio::Nexml::Factory - Bio::Phylo::Matrices::Datum |
+| * Bio::Nexml::Factory - Bio::Phylo::Matrices::Matrix |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| Bio-SamTools | * Bio::DB::Sam - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::Assembly::IO::sam - Bio::DB::Sam |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| BioPerl-Run | * Bio::Tools::Run::Bowtie - NA | None |
+| | * Bio::Tools::Run::Samtools - NA | |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::Assembly::IO::bowtie - Bio::Tools::Run::Bowtie |
+| * Bio::Assembly::IO::bowtie - Bio::Tools::Run::Samtools |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Convert-Binary-C | * Convert::Binary::C - Binary Data | None |
-| | Conversion using C Types | |
+| Convert-Binary-C | * Convert::Binary::C - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -93,8 +135,16 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| DBI | * DBI - Generic Database Interface | None |
-| | (see DBD modules) | |
+| DBD-SQLite | * DBD::SQLite - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::SeqFeature::Store::DBI::SQLite - DBD::SQLite |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| DBI | * DBI - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -102,6 +152,7 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::DB::GFF::Adaptor::dbi::caching_handle - DBI |
| * Bio::DB::SeqFeature::Store::DBI::mysql - DBI |
| * Bio::DB::SeqFeature::Store::DBI::Pg - DBI |
+| * Bio::DB::Taxonomy::sqlite - DBI |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
@@ -117,20 +168,55 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
+| Digest-MD5 | * Digest::MD5 - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::IndexedBase - Digest::MD5 |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| Encode | * Encode - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::SeqVersion::gi - Encode |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| Error | * Error - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::Root::Root - Error |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| GD | * GD - NA | None |
+| | * GD::Simple - NA | |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::Align::Graphics - GD |
+| * Bio::Align::Graphics - GD::Simple |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
| Graph | * Graph::Directed - NA | None |
-| | * Graph::Undirected - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::PhyloNetwork - Graph::Directed |
| * Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph::Directed |
-| * Bio::Assembly::Tools::ContigSpectrum - Graph::Undirected |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| HTML-Parser | * HTML::HeadParser - Parse <HEAD> | None |
-| | section of HTML documents | |
+| HTML-Parser | * HTML::HeadParser - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -140,8 +226,45 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| IO-String | * IO::String - IO::File interface | None |
-| | for in-core strings | |
+| HTML-TableExtract | * HTML::TableExtract - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::SeqVersion::gi - HTML::TableExtract |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| HTTP-Message | * HTTP::Request::Common - NA | None |
+| | * HTTP::Response - NA | |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::DBFetch - HTTP::Request::Common |
+| * Bio::DB::HIV - HTTP::Request::Common |
+| * Bio::DB::NCBIHelper - HTTP::Request::Common |
+| * Bio::DB::SwissProt - HTTP::Request::Common |
+| * Bio::DB::WebDBSeqI - HTTP::Request::Common |
+| * Bio::DB::Query::WebQuery - HTTP::Request::Common |
+| * Bio::Tools::Run::RemoteBlast - HTTP::Request::Common |
+| * Bio::DB::WebDBSeqI - HTTP::Response |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| IO-Compress | * Compress::Zlib - NA | None |
+| | * IO::Uncompress::Gunzip - NA | |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::DB::SeqFeature::Store - Compress::Zlib |
+| * Bio::Assembly::IO::bowtie - IO::Uncompress::Gunzip |
+| * Bio::Assembly::IO::sam - IO::Uncompress::Gunzip |
+ ==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| IO-String | * IO::String - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -151,7 +274,6 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::Index::Blast - IO::String |
| * Bio::Index::BlastTable - IO::String |
| * Bio::Index::Hmmer - IO::String |
-| * Bio::SearchIO::Writer::BSMLResultWriter - IO::String |
| * Bio::SeqIO::game::gameWriter - IO::String |
| * Bio::Tools::Analysis::DNA::ESEfinder - IO::String |
| * Bio::Tools::Analysis::Protein::Domcut - IO::String |
@@ -163,50 +285,46 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::Tools::Analysis::Protein::Sopma - IO::String |
| * Bio::Tools::Phylo::Molphy - IO::String |
| * Bio::Tools::Phylo::PAML - IO::String |
+| * Bio::Tools::Phylo::PAML::Codeml - IO::String |
| * Bio::Tools::Run::RemoteBlast - IO::String |
| * Bio::TreeIO::cluster - IO::String |
+| * Bio::TreeIO::nexml - IO::String |
| * Bio::TreeIO::nexus - IO::String |
| * Bio::Variation::IO::xml - IO::String |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Math-Random | * Math::Random - Random Number | None |
-| | Generators | |
+| MIME-Base64 | * MIME::Base64 - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::PhyloNetwork::RandomFactory - Math::Random |
+| * Bio::DB::SeqFeature::Store::DBI::Pg - MIME::Base64 |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Memoize | * Memoize - Automatically cache | None |
-| | results of functions | |
+| Memoize | * Memoize - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::DB::SeqFeature::Store::DBI::mysql - Memoize |
| * Bio::DB::SeqFeature::Store::DBI::Pg - Memoize |
+| * Bio::DB::SeqFeature::Store::DBI::SQLite - Memoize |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Module-Build | * Module::Build - Build, test, and | 0.2805 |
-| | install Perl modules | |
-| | * Module::Build::PPMMaker - NA | |
+| Module-Build | * Module::Build - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::Root::Build - Module::Build |
| * Bio::Root::Test - Module::Build |
-| * Bio::Root::Build - Module::Build::PPMMaker |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| PostScript | * PostScript::TextBlock - Objects | None |
-| | used by PS::Document | |
+| PostScript | * PostScript::TextBlock - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -215,8 +333,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| SVG | * SVG - Generate SVG images and | 2.26 |
-| | files | |
+| SVG | * SVG - NA | 2.26 |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -225,8 +342,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| SVG-Graph | * SVG::Graph - Series of Modules to | None |
-| | produce SVG graphs | |
+| SVG-Graph | * SVG::Graph - NA | None |
| | * SVG::Graph::Data - NA | |
| | * SVG::Graph::Data::Node - NA | |
| | * SVG::Graph::Data::Tree - NA | |
@@ -241,8 +357,7 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Set-Scalar | * Set::Scalar - Set of scalars (inc | None |
-| | references) | |
+| Set-Scalar | * Set::Scalar - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -251,39 +366,16 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Spreadsheet-ParseExcel | * Spreadsheet::ParseExcel - Get | None |
-| | information from Excel file | |
+| Spreadsheet-ParseExcel | * Spreadsheet::ParseExcel - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::Microarray::Tools::MitoChipV2Parser - Spreadsheet::ParseExcel |
-| * Bio::Microarray::Tools::ReseqChip - Spreadsheet::ParseExcel |
| * Bio::SeqIO::excel - Spreadsheet::ParseExcel |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Spreadsheet-WriteExcel | * Spreadsheet::WriteExcel - Write | None |
-| | cross-platform Excel binary file. | |
-|==============================================================================|
-| Used by: |
-|------------------------------------------------------------------------------|
-| * Bio::Microarray::Tools::ReseqChip - Spreadsheet::WriteExcel |
- ==============================================================================
- ==============================================================================
-| Distribution | Module used - Description | Min. ver. |
-|---------------------------+--------------------------------------+-----------|
-| Statistics-Frequency | * Statistics::Frequency - NA | None |
-|==============================================================================|
-| Used by: |
-|------------------------------------------------------------------------------|
-| * Bio::Microarray::Tools::ReseqChip - Statistics::Frequency |
- ==============================================================================
- ==============================================================================
-| Distribution | Module used - Description | Min. ver. |
-|---------------------------+--------------------------------------+-----------|
-| Storable | * Storable - Persistent data | None |
-| | structure mechanism | |
+| Storable | * Storable - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -293,34 +385,22 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Test-Exception | * Test::Exception - Functions for | None |
-| | testing exception-based code | |
+| Test-Most | * Test::Most - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::Root::Test - Test::Exception |
+| * Bio::Root::Test - Test::Most |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| Test-Simple | * Test::Builder - NA | None |
-| | * Test::More - More functions for | |
-| | writing tests | |
+| | * Test::Builder::Module - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::Root::Test::Warn - Test::Builder |
-| * Bio::Root::Test - Test::More |
- ==============================================================================
- ==============================================================================
-| Distribution | Module used - Description | Min. ver. |
-|---------------------------+--------------------------------------+-----------|
-| Test-Warn | * Test::Warn - NA | None |
-|==============================================================================|
-| Used by: |
-|------------------------------------------------------------------------------|
-| * Bio::Root::Test - Test::Warn |
-| * Bio::Root::Test::Warn - Test::Warn |
+| * Bio::Root::Test - Test::Builder |
+| * Bio::Root::Test - Test::Builder::Module |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
@@ -334,20 +414,18 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Time-HiRes | * Time::HiRes - High resolution | None |
-| | time, sleep, and alarm | |
+| Time-HiRes | * Time::HiRes - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
+| * Bio::DB::GenericWebAgent - Time::HiRes |
| * Bio::DB::SeqFeature::Store::Loader - Time::HiRes |
| * Bio::DB::SeqFeature::Store::DBI::mysql - Time::HiRes |
-| * Bio::DB::SeqFeature::Store::DBI::Pg - Time::HiRes |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| Tree-DAG_Node | * Tree::DAG_Node - base class for | None |
-| | trees | |
+| Tree-DAG_Node | * Tree::DAG_Node - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -357,25 +435,18 @@ NB: This list of packages is not authoritative. See the 'requires',
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| URI | * URI - NA | None |
-| | * URI::Escape - General URI | |
-| | escaping/unescaping functions | |
+| | * URI::Escape - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::DB::NCBIHelper - URI |
| * Bio::DB::Query::WebQuery - URI |
-| * Bio::Tools::EUtilities::EUtilParameters - URI |
| * Bio::DB::CUTG - URI::Escape |
-| * Bio::DB::Biblio::eutils - URI::Escape |
-| * Bio::FeatureIO::gff - URI::Escape |
-| * Bio::FeatureIO::interpro - URI::Escape |
-| * Bio::SeqFeature::Annotated - URI::Escape |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| WWW-Mechanize | * WWW::Mechanize - Automates web | None |
-| | page form & link interaction | |
+| WWW-Mechanize | * WWW::Mechanize - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
@@ -388,20 +459,17 @@ NB: This list of packages is not authoritative. See the 'requires',
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::DB::Fasta - Win32 |
| * Bio::DB::GFF - Win32 |
-| * Bio::DB::Qual - Win32 |
+| * Bio::DB::IndexedBase - Win32 |
| * Bio::Root::IO - Win32 |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-DOM | * XML::DOM - Implements Level 1 of | None |
-| | W3's DOM | |
+| XML-DOM | * XML::DOM - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::FeatureIO::interpro - XML::DOM |
| * Bio::SeqIO::bsml - XML::DOM |
| * Bio::SeqIO::interpro - XML::DOM |
==============================================================================
@@ -412,41 +480,31 @@ NB: This list of packages is not authoritative. See the 'requires',
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::FeatureIO::interpro - XML::DOM::XPath |
| * Bio::SeqIO::interpro - XML::DOM::XPath |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-LibXML | * XML::LibXML - Interface to the | None |
-| | libxml library | |
+| XML-LibXML | * XML::LibXML - NA | None |
| | * XML::LibXML::Reader - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
+| * Bio::SeqIO::seqxml - XML::LibXML |
| * Bio::TreeIO::phyloxml - XML::LibXML |
+| * Bio::SeqIO::seqxml - XML::LibXML::Reader |
| * Bio::TreeIO::phyloxml - XML::LibXML::Reader |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-Parser | * XML::Parser - Flexible fast | None |
-| | parser with plug-in styles | |
-|==============================================================================|
-| Used by: |
-|------------------------------------------------------------------------------|
-| * Bio::Biblio::IO::medlinexml - XML::Parser |
- ==============================================================================
- ==============================================================================
-| Distribution | Module used - Description | Min. ver. |
-|---------------------------+--------------------------------------+-----------|
| XML-SAX | * XML::SAX - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::ClusterIO::dbsnp - XML::SAX |
-| * Bio::SearchIO::blastxml - XML::SAX |
| * Bio::SeqIO::bsml_sax - XML::SAX |
+| * Bio::SeqIO::gbxml - XML::SAX |
| * Bio::SeqIO::tigrxml - XML::SAX |
==============================================================================
==============================================================================
@@ -461,38 +519,33 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-Simple | * XML::Simple - Easy API to | None |
-| | maintain XML (esp config files) | |
+| XML-Simple | * XML::Simple - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::DB::HIV::HIVQueryHelper - XML::Simple |
| * Bio::DB::Query::HIVQuery - XML::Simple |
-| * Bio::Tools::EUtilities - XML::Simple |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-Twig | * XML::Twig - A module for easy | None |
-| | processing of XML | |
+| XML-Twig | * XML::Twig - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::DB::Biblio::eutils - XML::Twig |
| * Bio::DB::Taxonomy::entrez - XML::Twig |
| * Bio::Variation::IO::xml - XML::Twig |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| XML-Writer | * XML::Writer - Module for writing | 0.4 |
-| | XML documents | |
+| XML-Writer | * XML::Writer - NA | 0.4 |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::SearchIO::Writer::BSMLResultWriter - XML::Writer |
| * Bio::SeqIO::agave - XML::Writer |
| * Bio::SeqIO::chadoxml - XML::Writer |
+| * Bio::SeqIO::seqxml - XML::Writer |
| * Bio::SeqIO::tinyseq - XML::Writer |
| * Bio::SeqIO::game::gameWriter - XML::Writer |
| * Bio::Variation::IO::xml - XML::Writer |
@@ -500,57 +553,19 @@ NB: This list of packages is not authoritative. See the 'requires',
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
-| bioperl-ext | * Bio::Ext::Align - NA | None |
-| | * Bio::SeqIO::staden::read - NA | |
-|==============================================================================|
-| Used by: |
-|------------------------------------------------------------------------------|
-| * Bio::SearchDist - Bio::Ext::Align |
-| * Bio::Tools::AlignFactory - Bio::Ext::Align |
-| * Bio::Tools::dpAlign - Bio::Ext::Align |
-| * Bio::Tools::pSW - Bio::Ext::Align |
-| * Bio::SeqIO::abi - Bio::SeqIO::staden::read |
-| * Bio::SeqIO::alf - Bio::SeqIO::staden::read |
-| * Bio::SeqIO::ctf - Bio::SeqIO::staden::read |
-| * Bio::SeqIO::exp - Bio::SeqIO::staden::read |
-| * Bio::SeqIO::pln - Bio::SeqIO::staden::read |
-| * Bio::SeqIO::ztr - Bio::SeqIO::staden::read |
- ==============================================================================
- ==============================================================================
-| Distribution | Module used - Description | Min. ver. |
-|---------------------------+--------------------------------------+-----------|
-| libwww-perl | * HTTP::Request - Class | 5.64 |
-| | encapsulating HTTP Requests | |
-| | * HTTP::Request::Common - Functions | |
-| | that generate HTTP::Requests | |
-| | * HTTP::Response - Class | |
-| | encapsulating HTTP Responses | |
-| | * LWP - Libwww-perl | |
-| | * LWP::Simple - Simple procedural | |
-| | interface to libwww-perl | |
-| | * LWP::UserAgent - A WWW UserAgent | |
-| | class | |
+| libwww-perl | * LWP - NA | 5.64 |
+| | * LWP::UserAgent - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
-| * Bio::Tools::EUtilities::EUtilParameters - HTTP::Request |
-| * Bio::DB::DBFetch - HTTP::Request::Common |
-| * Bio::DB::HIV - HTTP::Request::Common |
-| * Bio::DB::NCBIHelper - HTTP::Request::Common |
-| * Bio::DB::SwissProt - HTTP::Request::Common |
-| * Bio::DB::WebDBSeqI - HTTP::Request::Common |
-| * Bio::DB::Query::WebQuery - HTTP::Request::Common |
-| * Bio::Tools::Run::RemoteBlast - HTTP::Request::Common |
-| * Bio::DB::WebDBSeqI - HTTP::Response |
| * Bio::Tools::Protparam - LWP |
| * Bio::Tools::Run::RemoteBlast - LWP |
-| * Bio::DB::Biblio::eutils - LWP::Simple |
-| * Bio::Root::IO - LWP::Simple |
| * Bio::DB::GenericWebAgent - LWP::UserAgent |
| * Bio::DB::MeSH - LWP::UserAgent |
| * Bio::DB::WebDBSeqI - LWP::UserAgent |
| * Bio::DB::Query::WebQuery - LWP::UserAgent |
| * Bio::Root::Build - LWP::UserAgent |
+| * Bio::Root::IO - LWP::UserAgent |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
@@ -572,3 +587,13 @@ NB: This list of packages is not authoritative. See the 'requires',
|------------------------------------------------------------------------------|
| * Bio::DB::WebDBSeqI - Apache2::SubProcess |
==============================================================================
+ ==============================================================================
+| Distribution | Module used - Description | Min. ver. |
+|---------------------------+--------------------------------------+-----------|
+| version | * version - NA | None |
+|==============================================================================|
+| Used by: |
+|------------------------------------------------------------------------------|
+| * Bio::SeqIO::mbsout - version |
+| * Bio::SeqIO::msout - version |
+ ==============================================================================
diff --git a/INSTALL.md b/INSTALL.md
index ef5c3f7..856a711 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -7,29 +7,6 @@ Unix, Linux, and Mac OS X. For installing BioPerl on Windows, please
read INSTALL.WIN. The other way is to use a Docker image with a
BioPerl build, whether one we support or one you build yourself.
-# Using BioPerl via Docker
-
-If you don't have Docker installed already, instructions for [how to install Docker] on Linux, MacOSX, and Windows are available online.
-
-We officially support several builds (latest, stable, and releases)
-hosted in the [bioperl/bioperl] repo on Docker Hub. These images do not
-have a pre-defined entrypoint. If you have a BioPerl script in the
-current directory, you can run it as simple as this:
-
-```
-docker run -t --rm -v `pwd`:/work -w /work bioperl/bioperl perl my-script.pl
-```
-
-Or run an interactive shell:
-
-```
-docker run -ti --rm -v `pwd`:/work -w /work bioperl/bioperl bash
-```
-
-You can also build your own Docker image of BioPerl, using the same
-base image and pre-built dependencies that we use. Simply build off of
-the [bioperl/bioperl-deps] image.
-
# Installing BioPerl locally
Note that this documentation is for Unix, Linux, and MacOSX. For installing BioPerl on Windows, please read INSTALL.WIN.
@@ -39,7 +16,7 @@ Note that this documentation is for Unix, Linux, and MacOSX. For installing BioP
* `Perl 5.6.1 or higher` Version 5.10 or higher is highly
recommended. Modules are tested against version 5.14 and
above.
- * `make` For Mac OS X, this requires installing the Xcode Developer
+ * `make` For Mac OS X, this requires installing the Xcode Developer
Tools.
## Preliminary Preparation
@@ -103,29 +80,29 @@ Then find the name of the latest BioPerl package:
cpan>d /bioperl/
....
- Distribution CJFIELDS/BioPerl-1.6.901.tar.gz
- Distribution CJFIELDS/BioPerl-1.6.922.tar.gz
- Distribution CJFIELDS/BioPerl-1.6.924.tar.gz
+ Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
+ Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
+ Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
```
And install the most recent:
```
-cpan>install CJFIELDS/BioPerl-1.6.924.tar.gz
+cpan>install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
```
If you've installed everything perfectly and all the network
connections are working then you will pass all the tests run in the
-`./Build test` phase. Sometimes you may see a failed test. Remember that
-there are over 900 modules in BioPerl and the test suite is running more
-than 12000 individual tests, a failed test may not affect your usage
+`./Build test` phase. Sometimes you may see a failed test. Remember that
+there are over 900 modules in BioPerl and the test suite is running more
+than 12000 individual tests, a failed test may not affect your usage
of BioPerl.
-If there's a failed test and you think that the failed test will not
+If there's a failed test and you think that the failed test will not
affect how you intend to use BioPerl then do:
```
-cpan>force install C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
+cpan>force install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
```
If you're concerned about a failed test and need assistance or advice
@@ -135,9 +112,9 @@ results of the failed install.
## Installing BioPerl from Github
**NOTE:** We generally do not recommend installing the latest code from Github
-unless you absolutely need the latest bug fixes.
+unless you absolutely need the latest bug fixes.
-The very latest version of Bioperl is at github.com. If you want this
+The very latest version of Bioperl is at github.com. If you want this
version then download it from https://github.com/bioperl/bioperl-live as a
`tar.gz` or `zip` file, or retrieve it using the command line:
@@ -179,7 +156,7 @@ Install:
./Build install
```
-You may need root permissions in order to run `./Build install`, so you
+You may need root permissions in order to run `./Build install`, so you
will want to talk to your systems manager if you don't have the necessary
privileges. Or you can install the package in your own home
directory, see INSTALLING BIOPERL USING `local::lib`.
@@ -191,11 +168,11 @@ system directories you can install them in your home directory
using [local::lib](https://metacpan.org/pod/local::lib). The instructions for first installing
`local::lib` are found in the link.
-Once `local::lib` is installed you can install BioPerl using a
+Once `local::lib` is installed you can install BioPerl using a
command like this:
```
-perl -MCPAN -Mlocal::lib -e 'CPAN::install(C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz)'
+perl -MCPAN -Mlocal::lib -e 'CPAN::install(C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz)'
```
## Installing BioPerl Scripts
@@ -225,7 +202,7 @@ the Seq test you would type:
./Build test --test_files t/Seq/Seq.t --verbose
```
-The `--test_files` argument can be used multiple times to try a set of test
+The `--test_files` argument can be used multiple times to try a set of test
scripts in one go. The `--verbose` arguement outputs the detailed test results, instead of just the summary you see during `./Build test`.
The `--test-files` argument can also work as a glob. For instance, to run tests on all SearchIO modules, use the following:
@@ -238,7 +215,7 @@ You can also use the command-line tool `prove` to run tests as well, which
is quite useful if you are developing code:
```
-prove -lrv t/SearchIO*
+prove -lrv t/SearchIO*
```
If you are trying to learn how to use a module, often the test suite
@@ -260,3 +237,27 @@ distribution until adequate tests are added and the API stablizes.
[how to install Docker]: https://docs.docker.com/engine/installation/
[bioperl/bioperl]: https://hub.docker.com/r/bioperl/bioperl/
[bioperl/bioperl-deps]: https://hub.docker.com/r/bioperl/bioperl-deps/
+
+# Using BioPerl via Docker
+
+If you don't have Docker installed already, instructions for [how to install Docker] on Linux, MacOSX, and Windows are available online.
+
+We officially support several builds (latest, stable, and releases)
+hosted in the [bioperl/bioperl] repo on Docker Hub. These images do not
+have a pre-defined entrypoint. If you have a BioPerl script in the
+current directory, you can run it as simple as this:
+
+```
+docker run -t --rm -v `pwd`:/work -w /work bioperl/bioperl perl my-script.pl
+```
+
+Or run an interactive shell:
+
+```
+docker run -ti --rm -v `pwd`:/work -w /work bioperl/bioperl bash
+```
+
+You can also build your own Docker image of BioPerl, using the same
+base image and pre-built dependencies that we use. Simply build off of
+the [bioperl/bioperl-deps] image.
+
diff --git a/MANIFEST b/MANIFEST
index f57b215..6a5b243 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -710,10 +710,6 @@ Bio/Tools/Phylo/Gerp.pm
Bio/Tools/Phylo/Gumby.pm
Bio/Tools/Phylo/Molphy.pm
Bio/Tools/Phylo/Molphy/Result.pm
-Bio/Tools/Phylo/PAML.pm
-Bio/Tools/Phylo/PAML/Codeml.pm
-Bio/Tools/Phylo/PAML/ModelResult.pm
-Bio/Tools/Phylo/PAML/Result.pm
Bio/Tools/Phylo/Phylip/ProtDist.pm
Bio/Tools/pICalculator.pm
Bio/Tools/Prediction/Exon.pm
@@ -998,7 +994,6 @@ scripts/utilities/bp_mrtrans.pl
scripts/utilities/bp_mutate.pl
scripts/utilities/bp_netinstall.pl
scripts/utilities/bp_nrdb.pl
-scripts/utilities/bp_pairwise_kaks.pl
scripts/utilities/bp_remote_blast.pl
scripts/utilities/bp_revtrans-motif.pl
scripts/utilities/bp_search2alnblocks.pl
@@ -1074,8 +1069,6 @@ t/data/5X_1895.FASTXY
t/data/8HVP.pdb
t/data/a_thaliana.blastn
t/data/AAC12660.fa
-t/data/aaml.mlc
-t/data/aaml_pairwise.mlc
t/data/AB077698.gb
t/data/acefile.ace.1
t/data/acefile.singlets
@@ -1106,8 +1099,6 @@ t/data/bad_dbfa/bug3172.fa
t/data/bad_dbfa/shotdb.fa
t/data/badfasta.fa
t/data/barns-combined.nex
-t/data/baseml.pairwise
-t/data/baseml.usertree
t/data/basic-bush.nex
t/data/basic-ladder.nex
t/data/BC000007.gbk
@@ -1137,7 +1128,6 @@ t/data/blosum62.bla
t/data/BN000066-tpa.embl
t/data/bootstrap.tre
t/data/BOSS_DROME.FASTP_v35_04
-t/data/branchSite.mlc
t/data/brassica_ATH.WUBLASTN
t/data/bug1986.blast2
t/data/bug1986.blastp
@@ -1156,7 +1146,6 @@ t/data/bug2982.embl
t/data/bug2982.gb
t/data/bug3021.gmap
t/data/bug3086.embl
-t/data/bug3331.mlc
t/data/c200-vs-yeast.BLASTN
t/data/c200-vs-yeast.BLASTN.m8
t/data/calm.swiss
@@ -1173,27 +1162,7 @@ t/data/characters.nexml.old.xml
t/data/cmsearch.multi.out
t/data/cmsearch.nohit.out
t/data/cmsearch_output.txt
-t/data/codeml.mlc
-t/data/codeml315.mlc
-t/data/codeml4.mlc
-t/data/codeml43.mlc
-t/data/codeml43_nssites.mlc
-t/data/codeml45.mlc
t/data/codeml45b.mlc
-t/data/codeml_lysozyme/2NG.dN
-t/data/codeml_lysozyme/2NG.dS
-t/data/codeml_lysozyme/2NG.tt
-t/data/codeml_lysozyme/4fold.nuc
-t/data/codeml_lysozyme/lnf
-t/data/codeml_lysozyme/lysozymeSmall.ctl
-t/data/codeml_lysozyme/lysozymeSmall.trees
-t/data/codeml_lysozyme/lysozymeSmall.txt
-t/data/codeml_lysozyme/mlc
-t/data/codeml_lysozyme/rst
-t/data/codeml_lysozyme/rst1
-t/data/codeml_lysozyme/rub
-t/data/codeml_nan.mlc
-t/data/codeml_nssites.mlc
t/data/compLD_missingtest.prettybase
t/data/compLD_test.prettybase
t/data/component.ontology.test
@@ -1419,7 +1388,6 @@ t/data/lucy.seq
t/data/lucy.stderr
t/data/lysozyme6.protml
t/data/lysozyme6.simple.protml
-t/data/M0.mlc
t/data/M12730.gb
t/data/map_hem/HEM1-HEM12.fa
t/data/map_hem/HEM1-HEM12.fa.revcom
@@ -1595,6 +1563,7 @@ t/data/prints.out
t/data/promoterwise.out
t/data/protpars.phy
t/data/protpars_longid.phy
+t/data/ps_scan/out.PrositeScan
t/data/pseudowise.out
t/data/psi_xml.dat
t/data/psiblastreport.out
@@ -1634,6 +1603,7 @@ t/data/seg.out
t/data/semicolon.newick
t/data/seqdatabase.ini
t/data/seqfeaturedb/test.gff3
+t/data/seqfile-no-desc.pir
t/data/seqfile.pir
t/data/seqs.fas
t/data/sequencefamily.dat
@@ -1650,7 +1620,6 @@ t/data/signalp.summary
t/data/sim4.for.for
t/data/sim4.for.rev
t/data/sim4.rev
-t/data/singleNSsite.mlc
t/data/singlescore.gbk
t/data/singlet_w_CT.ace
t/data/so.obo
@@ -1799,8 +1768,6 @@ t/data/withrefm.906
t/data/worm_fam_2785.cdna
t/data/X98338_Adh-mRNA.gb
t/data/yeast.tRNAscanSE
-t/data/yn00.mlc
-t/data/yn00_45.mlc
t/data/YP_007988852.gp
t/data/ZABJ4EA7014.CH878695.1.blast.txt
t/Draw/Pictogram.t
@@ -2039,11 +2006,11 @@ t/Tools/Lucy.t
t/Tools/Match.t
t/Tools/Phylo/Gerp.t
t/Tools/Phylo/Molphy.t
-t/Tools/Phylo/PAML.t
t/Tools/Phylo/Phylip/ProtDist.t
t/Tools/pICalculator.t
t/Tools/Primer3.t
t/Tools/Promoterwise.t
+t/Tools/PrositeScan.t
t/Tools/Pseudowise.t
t/Tools/QRNA.t
t/Tools/RandDistFunctions.t
diff --git a/META.json b/META.json
index 4baa04f..607c098 100644
--- a/META.json
+++ b/META.json
@@ -4,7 +4,7 @@
"BioPerl Team <bioperl-l at bioperl.org>"
],
"dynamic_config" : 1,
- "generated_by" : "Module::Build version 0.4218",
+ "generated_by" : "Module::Build version 0.4224",
"license" : [
"perl_5"
],
@@ -81,727 +81,727 @@
"provides" : {
"Bio::Align::AlignI" : {
"file" : "Bio/Align/AlignI.pm",
- "version" : "1.007001"
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+ "version" : "1.007002"
},
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- "version" : "1.007001"
+ "version" : "1.007002"
},
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},
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+ "version" : "1.007002"
},
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+ "version" : "1.007002"
},
"Bio::DB::SeqFeature::Store::LoadHelper" : {
"file" : "Bio/DB/SeqFeature/Store/LoadHelper.pm",
@@ -809,2487 +809,2471 @@
},
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"file" : "Bio/DB/SeqFeature/Store/Loader.pm",
- "version" : "1.007001"
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+ "version" : "1.007002"
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+ "version" : "1.007002"
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},
"FeatureStore" : {
"file" : "Bio/DB/GFF/Adaptor/berkeleydb.pm",
- "version" : "1.007001"
+ "version" : "1.007002"
}
},
"release_status" : "stable",
@@ -3298,5 +3282,6 @@
"http://dev.perl.org/licenses/"
]
},
- "version" : "1.007001"
+ "version" : "1.007002",
+ "x_serialization_backend" : "JSON::PP version 2.27300_01"
}
diff --git a/META.yml b/META.yml
index e36d406..bf4b6b7 100644
--- a/META.yml
+++ b/META.yml
@@ -11,7 +11,7 @@ build_requires:
configure_requires:
Module::Build: '0.42'
dynamic_config: 1
-generated_by: 'Module::Build version 0.4218, CPAN::Meta::Converter version 2.150001'
+generated_by: 'Module::Build version 0.4224, CPAN::Meta::Converter version 2.150005'
license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -20,2413 +20,2401 @@ name: BioPerl
provides:
Bio::Align::AlignI:
file: Bio/Align/AlignI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::DNAStatistics:
file: Bio/Align/DNAStatistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::Graphics:
file: Bio/Align/Graphics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::PairwiseStatistics:
file: Bio/Align/PairwiseStatistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::ProteinStatistics:
file: Bio/Align/ProteinStatistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::StatisticsI:
file: Bio/Align/StatisticsI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Align::Utilities:
file: Bio/Align/Utilities.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO:
file: Bio/AlignIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::Handler::GenericAlignHandler:
file: Bio/AlignIO/Handler/GenericAlignHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::arp:
file: Bio/AlignIO/arp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::bl2seq:
file: Bio/AlignIO/bl2seq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::clustalw:
file: Bio/AlignIO/clustalw.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::emboss:
file: Bio/AlignIO/emboss.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::fasta:
file: Bio/AlignIO/fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::largemultifasta:
file: Bio/AlignIO/largemultifasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::maf:
file: Bio/AlignIO/maf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::mase:
file: Bio/AlignIO/mase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::mega:
file: Bio/AlignIO/mega.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::meme:
file: Bio/AlignIO/meme.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::metafasta:
file: Bio/AlignIO/metafasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::msf:
file: Bio/AlignIO/msf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::nexml:
file: Bio/AlignIO/nexml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::nexus:
file: Bio/AlignIO/nexus.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::pfam:
file: Bio/AlignIO/pfam.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::phylip:
file: Bio/AlignIO/phylip.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::po:
file: Bio/AlignIO/po.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::proda:
file: Bio/AlignIO/proda.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::prodom:
file: Bio/AlignIO/prodom.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::psi:
file: Bio/AlignIO/psi.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::selex:
file: Bio/AlignIO/selex.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::stockholm:
file: Bio/AlignIO/stockholm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AlignIO::xmfa:
file: Bio/AlignIO/xmfa.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnalysisI:
file: Bio/AnalysisI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnalysisI::JobI:
file: Bio/AnalysisI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnalysisParserI:
file: Bio/AnalysisParserI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnalysisResultI:
file: Bio/AnalysisResultI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnnotatableI:
file: Bio/AnnotatableI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::AnnotationFactory:
file: Bio/Annotation/AnnotationFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Collection:
file: Bio/Annotation/Collection.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Comment:
file: Bio/Annotation/Comment.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::DBLink:
file: Bio/Annotation/DBLink.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::OntologyTerm:
file: Bio/Annotation/OntologyTerm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Reference:
file: Bio/Annotation/Reference.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Relation:
file: Bio/Annotation/Relation.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::SimpleValue:
file: Bio/Annotation/SimpleValue.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::StructuredValue:
file: Bio/Annotation/StructuredValue.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::TagTree:
file: Bio/Annotation/TagTree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Target:
file: Bio/Annotation/Target.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::Tree:
file: Bio/Annotation/Tree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Annotation::TypeManager:
file: Bio/Annotation/TypeManager.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnnotationCollectionI:
file: Bio/AnnotationCollectionI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::AnnotationI:
file: Bio/AnnotationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::Contig:
file: Bio/Assembly/Contig.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::ContigAnalysis:
file: Bio/Assembly/ContigAnalysis.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO:
file: Bio/Assembly/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::ace:
file: Bio/Assembly/IO/ace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::bowtie:
file: Bio/Assembly/IO/bowtie.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::maq:
file: Bio/Assembly/IO/maq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::phrap:
file: Bio/Assembly/IO/phrap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::sam:
file: Bio/Assembly/IO/sam.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::IO::tigr:
file: Bio/Assembly/IO/tigr.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::Scaffold:
file: Bio/Assembly/Scaffold.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::ScaffoldI:
file: Bio/Assembly/ScaffoldI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::Singlet:
file: Bio/Assembly/Singlet.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Assembly::Tools::ContigSpectrum:
file: Bio/Assembly/Tools/ContigSpectrum.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Cluster::ClusterFactory:
file: Bio/Cluster/ClusterFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Cluster::FamilyI:
file: Bio/Cluster/FamilyI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Cluster::SequenceFamily:
file: Bio/Cluster/SequenceFamily.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Cluster::UniGene:
file: Bio/Cluster/UniGene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Cluster::UniGeneI:
file: Bio/Cluster/UniGeneI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::ClusterI:
file: Bio/ClusterI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::ClusterIO:
file: Bio/ClusterIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::ClusterIO::dbsnp:
file: Bio/ClusterIO/dbsnp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::ClusterIO::unigene:
file: Bio/ClusterIO/unigene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::CodonUsage::IO:
file: Bio/CodonUsage/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::CodonUsage::Table:
file: Bio/CodonUsage/Table.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Ace:
file: Bio/DB/Ace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::BioFetch:
file: Bio/DB/BioFetch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::CUTG:
file: Bio/DB/CUTG.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::DBFetch:
file: Bio/DB/DBFetch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::EMBL:
file: Bio/DB/EMBL.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::EntrezGene:
file: Bio/DB/EntrezGene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Expression:
file: Bio/DB/Expression.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Expression::geo:
file: Bio/DB/Expression/geo.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Failover:
file: Bio/DB/Failover.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Fasta:
file: Bio/DB/Fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Fasta::Subdir:
file: Bio/DB/SeqFeature/Store/berkeleydb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::FileCache:
file: Bio/DB/FileCache.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat:
file: Bio/DB/Flat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BDB:
file: Bio/DB/Flat/BDB.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BDB::embl:
file: Bio/DB/Flat/BDB/embl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BDB::fasta:
file: Bio/DB/Flat/BDB/fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BDB::genbank:
file: Bio/DB/Flat/BDB/genbank.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BDB::swiss:
file: Bio/DB/Flat/BDB/swiss.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Flat::BinarySearch:
file: Bio/DB/Flat/BinarySearch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF:
file: Bio/DB/GFF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::ace:
file: Bio/DB/GFF/Adaptor/ace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::berkeleydb:
file: Bio/DB/GFF/Adaptor/berkeleydb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::berkeleydb::iterator:
file: Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::biofetch:
file: Bio/DB/GFF/Adaptor/biofetch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::biofetch_oracle:
file: Bio/DB/GFF/Adaptor/biofetch_oracle.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi:
file: Bio/DB/GFF/Adaptor/dbi.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::caching_handle:
file: Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::faux_dbh:
file: Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::iterator:
file: Bio/DB/GFF/Adaptor/dbi/iterator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::mysql:
file: Bio/DB/GFF/Adaptor/dbi/mysql.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::mysqlace:
file: Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::mysqlcmap:
file: Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::mysqlopt:
file: Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::oracle:
file: Bio/DB/GFF/Adaptor/dbi/oracle.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::oracleace:
file: Bio/DB/GFF/Adaptor/dbi/oracleace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::pg:
file: Bio/DB/GFF/Adaptor/dbi/pg.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::dbi::pg_fts:
file: Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::memory:
file: Bio/DB/GFF/Adaptor/memory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::memory::feature_serializer:
file: Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Adaptor::memory::iterator:
file: Bio/DB/GFF/Adaptor/memory/iterator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator:
file: Bio/DB/GFF/Aggregator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::alignment:
file: Bio/DB/GFF/Aggregator/alignment.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::clone:
file: Bio/DB/GFF/Aggregator/clone.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::coding:
file: Bio/DB/GFF/Aggregator/coding.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::gene:
file: Bio/DB/GFF/Aggregator/gene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::match:
file: Bio/DB/GFF/Aggregator/match.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::none:
file: Bio/DB/GFF/Aggregator/none.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::orf:
file: Bio/DB/GFF/Aggregator/orf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::processed_transcript:
file: Bio/DB/GFF/Aggregator/processed_transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::so_transcript:
file: Bio/DB/GFF/Aggregator/so_transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::transcript:
file: Bio/DB/GFF/Aggregator/transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_acembly:
file: Bio/DB/GFF/Aggregator/ucsc_acembly.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_ensgene:
file: Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_genscan:
file: Bio/DB/GFF/Aggregator/ucsc_genscan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_refgene:
file: Bio/DB/GFF/Aggregator/ucsc_refgene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_sanger22:
file: Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo:
file: Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_softberry:
file: Bio/DB/GFF/Aggregator/ucsc_softberry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_twinscan:
file: Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Aggregator::ucsc_unigene:
file: Bio/DB/GFF/Aggregator/ucsc_unigene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Featname:
file: Bio/DB/GFF/Featname.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Feature:
file: Bio/DB/GFF/Feature.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::FeatureIterator:
file: Bio/DB/GFF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Homol:
file: Bio/DB/GFF/Homol.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::ID_Iterator:
file: Bio/DB/GFF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::RelSegment:
file: Bio/DB/GFF/RelSegment.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Segment:
file: Bio/DB/GFF/Segment.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Typename:
file: Bio/DB/GFF/Typename.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Util::Binning:
file: Bio/DB/GFF/Util/Binning.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GFF::Util::Rearrange:
file: Bio/DB/GFF/Util/Rearrange.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GenBank:
file: Bio/DB/GenBank.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GenPept:
file: Bio/DB/GenPept.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::GenericWebAgent:
file: Bio/DB/GenericWebAgent.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::HIV:
file: Bio/DB/HIV.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::HIV::HIVAnnotProcessor:
file: Bio/DB/HIV/HIVAnnotProcessor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::HIV::HIVQueryHelper:
file: Bio/DB/HIV/HIVQueryHelper.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::InMemoryCache:
file: Bio/DB/InMemoryCache.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Indexed::Stream:
file: Bio/DB/IndexedBase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::IndexedBase:
file: Bio/DB/IndexedBase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::LocationI:
file: Bio/DB/LocationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::MeSH:
file: Bio/DB/MeSH.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::NCBIHelper:
file: Bio/DB/NCBIHelper.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Qual:
file: Bio/DB/Qual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Query::GenBank:
file: Bio/DB/Query/GenBank.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Query::HIVQuery:
file: Bio/DB/Query/HIVQuery.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Query::WebQuery:
file: Bio/DB/Query/WebQuery.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::QueryI:
file: Bio/DB/QueryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::RandomAccessI:
file: Bio/DB/RandomAccessI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::RefSeq:
file: Bio/DB/RefSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::ReferenceI:
file: Bio/DB/ReferenceI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Registry:
file: Bio/DB/Registry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature:
file: Bio/DB/SeqFeature.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::NormalizedFeature:
file: Bio/DB/SeqFeature/NormalizedFeature.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::NormalizedFeatureI:
file: Bio/DB/SeqFeature/NormalizedFeatureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::NormalizedTableFeatureI:
file: Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Segment:
file: Bio/DB/SeqFeature/Segment.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store:
file: Bio/DB/SeqFeature/Store.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::DBI::Iterator:
file: Bio/DB/SeqFeature/Store/DBI/Iterator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::DBI::Pg:
file: Bio/DB/SeqFeature/Store/DBI/Pg.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::DBI::SQLite:
file: Bio/DB/SeqFeature/Store/DBI/SQLite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::DBI::mysql:
file: Bio/DB/SeqFeature/Store/DBI/mysql.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::FeatureFileLoader:
file: Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::FeatureIterator:
file: Bio/DB/SeqFeature/Store.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::GFF2Loader:
file: Bio/DB/SeqFeature/Store/GFF2Loader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::GFF3Loader:
file: Bio/DB/SeqFeature/Store/GFF3Loader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::LoadHelper:
file: Bio/DB/SeqFeature/Store/LoadHelper.pm
version: '1.12'
Bio::DB::SeqFeature::Store::Loader:
file: Bio/DB/SeqFeature/Store/Loader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::bdb:
file: Bio/DB/SeqFeature/Store/bdb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::berkeleydb:
file: Bio/DB/SeqFeature/Store/berkeleydb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::berkeleydb3:
file: Bio/DB/SeqFeature/Store/berkeleydb3.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::berkeleydb::Iterator:
file: Bio/DB/SeqFeature/Store/berkeleydb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::memory:
file: Bio/DB/SeqFeature/Store/memory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqFeature::Store::memory::Iterator:
file: Bio/DB/SeqFeature/Store/memory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqI:
file: Bio/DB/SeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqVersion:
file: Bio/DB/SeqVersion.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SeqVersion::gi:
file: Bio/DB/SeqVersion/gi.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::SwissProt:
file: Bio/DB/SwissProt.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::TFBS:
file: Bio/DB/TFBS.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::TFBS::transfac_pro:
file: Bio/DB/TFBS/transfac_pro.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy:
file: Bio/DB/Taxonomy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::entrez:
file: Bio/DB/Taxonomy/entrez.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::flatfile:
file: Bio/DB/Taxonomy/flatfile.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::greengenes:
file: Bio/DB/Taxonomy/greengenes.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::list:
file: Bio/DB/Taxonomy/list.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::silva:
file: Bio/DB/Taxonomy/silva.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Taxonomy::sqlite:
file: Bio/DB/Taxonomy/sqlite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::Universal:
file: Bio/DB/Universal.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::UpdateableSeqI:
file: Bio/DB/UpdateableSeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DB::WebDBSeqI:
file: Bio/DB/WebDBSeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DBLinkContainerI:
file: Bio/DBLinkContainerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Das::FeatureTypeI:
file: Bio/Das/FeatureTypeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Das::SegmentI:
file: Bio/Das/SegmentI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DasI:
file: Bio/DasI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::DescribableI:
file: Bio/DescribableI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Draw::Pictogram:
file: Bio/Draw/Pictogram.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Event::EventGeneratorI:
file: Bio/Event/EventGeneratorI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Event::EventHandlerI:
file: Bio/Event/EventHandlerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::AnalysisI:
file: Bio/Factory/AnalysisI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::ApplicationFactoryI:
file: Bio/Factory/ApplicationFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::DriverFactory:
file: Bio/Factory/DriverFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::FTLocationFactory:
file: Bio/Factory/FTLocationFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::LocationFactoryI:
file: Bio/Factory/LocationFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::MapFactoryI:
file: Bio/Factory/MapFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::ObjectBuilderI:
file: Bio/Factory/ObjectBuilderI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::ObjectFactory:
file: Bio/Factory/ObjectFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::ObjectFactoryI:
file: Bio/Factory/ObjectFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::SeqAnalysisParserFactory:
file: Bio/Factory/SeqAnalysisParserFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::SeqAnalysisParserFactoryI:
file: Bio/Factory/SeqAnalysisParserFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::SequenceFactoryI:
file: Bio/Factory/SequenceFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::SequenceProcessorI:
file: Bio/Factory/SequenceProcessorI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::SequenceStreamI:
file: Bio/Factory/SequenceStreamI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Factory::TreeFactoryI:
file: Bio/Factory/TreeFactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::FeatureHolderI:
file: Bio/FeatureHolderI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::HandlerBaseI:
file: Bio/HandlerBaseI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::IdCollectionI:
file: Bio/IdCollectionI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::IdentifiableI:
file: Bio/IdentifiableI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Abstract:
file: Bio/Index/Abstract.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::AbstractSeq:
file: Bio/Index/AbstractSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Blast:
file: Bio/Index/Blast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::BlastTable:
file: Bio/Index/BlastTable.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::EMBL:
file: Bio/Index/EMBL.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Fasta:
file: Bio/Index/Fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Fastq:
file: Bio/Index/Fastq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::GenBank:
file: Bio/Index/GenBank.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Hmmer:
file: Bio/Index/Hmmer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Qual:
file: Bio/Index/Qual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Stockholm:
file: Bio/Index/Stockholm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::SwissPfam:
file: Bio/Index/SwissPfam.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Index::Swissprot:
file: Bio/Index/Swissprot.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::AARange:
file: Bio/LiveSeq/AARange.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Chain:
file: Bio/LiveSeq/Chain.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::ChainI:
file: Bio/LiveSeq/ChainI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::DNA:
file: Bio/LiveSeq/DNA.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Exon:
file: Bio/LiveSeq/Exon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Gene:
file: Bio/LiveSeq/Gene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::IO::BioPerl:
file: Bio/LiveSeq/IO/BioPerl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::IO::Loader:
file: Bio/LiveSeq/IO/Loader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Intron:
file: Bio/LiveSeq/Intron.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Mutation:
file: Bio/LiveSeq/Mutation.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Mutator:
file: Bio/LiveSeq/Mutator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Prim_Transcript:
file: Bio/LiveSeq/Prim_Transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Range:
file: Bio/LiveSeq/Range.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Repeat_Region:
file: Bio/LiveSeq/Repeat_Region.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Repeat_Unit:
file: Bio/LiveSeq/Repeat_Unit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::SeqI:
file: Bio/LiveSeq/SeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Transcript:
file: Bio/LiveSeq/Transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LiveSeq::Translation:
file: Bio/LiveSeq/Translation.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LocatableSeq:
file: Bio/LocatableSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::Atomic:
file: Bio/Location/Atomic.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::AvWithinCoordPolicy:
file: Bio/Location/AvWithinCoordPolicy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::CoordinatePolicyI:
file: Bio/Location/CoordinatePolicyI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::Fuzzy:
file: Bio/Location/Fuzzy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::FuzzyLocationI:
file: Bio/Location/FuzzyLocationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::NarrowestCoordPolicy:
file: Bio/Location/NarrowestCoordPolicy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::Simple:
file: Bio/Location/Simple.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::Split:
file: Bio/Location/Split.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::SplitLocationI:
file: Bio/Location/SplitLocationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Location::WidestCoordPolicy:
file: Bio/Location/WidestCoordPolicy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::LocationI:
file: Bio/LocationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Clone:
file: Bio/Map/Clone.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Contig:
file: Bio/Map/Contig.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::CytoMap:
file: Bio/Map/CytoMap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::CytoMarker:
file: Bio/Map/CytoMarker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::CytoPosition:
file: Bio/Map/CytoPosition.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::EntityI:
file: Bio/Map/EntityI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::FPCMarker:
file: Bio/Map/FPCMarker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Gene:
file: Bio/Map/Gene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::GeneMap:
file: Bio/Map/GeneMap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::GenePosition:
file: Bio/Map/GenePosition.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::GeneRelative:
file: Bio/Map/GeneRelative.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::LinkageMap:
file: Bio/Map/LinkageMap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::LinkagePosition:
file: Bio/Map/LinkagePosition.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::MapI:
file: Bio/Map/MapI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Mappable:
file: Bio/Map/Mappable.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::MappableI:
file: Bio/Map/MappableI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Marker:
file: Bio/Map/Marker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::MarkerI:
file: Bio/Map/MarkerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Microsatellite:
file: Bio/Map/Microsatellite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::OrderedPosition:
file: Bio/Map/OrderedPosition.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::OrderedPositionWithDistance:
file: Bio/Map/OrderedPositionWithDistance.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Physical:
file: Bio/Map/Physical.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Position:
file: Bio/Map/Position.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::PositionHandler:
file: Bio/Map/PositionHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::PositionHandlerI:
file: Bio/Map/PositionHandlerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::PositionI:
file: Bio/Map/PositionI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::PositionWithSequence:
file: Bio/Map/PositionWithSequence.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Prediction:
file: Bio/Map/Prediction.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::Relative:
file: Bio/Map/Relative.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::RelativeI:
file: Bio/Map/RelativeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::SimpleMap:
file: Bio/Map/SimpleMap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Map::TranscriptionFactor:
file: Bio/Map/TranscriptionFactor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::MapIO:
file: Bio/MapIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::MapIO::fpc:
file: Bio/MapIO/fpc.pm
- version: '1.007001'
+ version: '1.007002'
Bio::MapIO::mapmaker:
file: Bio/MapIO/mapmaker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::Generic:
file: Bio/Matrix/Generic.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::IO:
file: Bio/Matrix/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::IO::mlagan:
file: Bio/Matrix/IO/mlagan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::IO::phylip:
file: Bio/Matrix/IO/phylip.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::IO::scoring:
file: Bio/Matrix/IO/scoring.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::MatrixI:
file: Bio/Matrix/MatrixI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::Mlagan:
file: Bio/Matrix/Mlagan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO:
file: Bio/Matrix/PSM/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO::mast:
file: Bio/Matrix/PSM/IO/mast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO::masta:
file: Bio/Matrix/PSM/IO/masta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO::meme:
file: Bio/Matrix/PSM/IO/meme.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO::psiblast:
file: Bio/Matrix/PSM/IO/psiblast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::IO::transfac:
file: Bio/Matrix/PSM/IO/transfac.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::InstanceSite:
file: Bio/Matrix/PSM/InstanceSite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::InstanceSiteI:
file: Bio/Matrix/PSM/InstanceSiteI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::ProtMatrix:
file: Bio/Matrix/PSM/ProtMatrix.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::ProtPsm:
file: Bio/Matrix/PSM/ProtPsm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::Psm:
file: Bio/Matrix/PSM/Psm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::PsmHeader:
file: Bio/Matrix/PSM/PsmHeader.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::PsmHeaderI:
file: Bio/Matrix/PSM/PsmHeaderI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::PsmI:
file: Bio/Matrix/PSM/PsmI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::SiteMatrix:
file: Bio/Matrix/PSM/SiteMatrix.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PSM::SiteMatrixI:
file: Bio/Matrix/PSM/SiteMatrixI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::PhylipDist:
file: Bio/Matrix/PhylipDist.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Matrix::Scoring:
file: Bio/Matrix/Scoring.pm
- version: '1.007001'
+ version: '1.007002'
Bio::MolEvol::CodonModel:
file: Bio/MolEvol/CodonModel.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Nexml::Factory:
file: Bio/Nexml/Factory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::NexmlIO:
file: Bio/NexmlIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::DocumentRegistry:
file: Bio/Ontology/DocumentRegistry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::GOterm:
file: Bio/Ontology/GOterm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::InterProTerm:
file: Bio/Ontology/InterProTerm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::OBOEngine:
file: Bio/Ontology/OBOEngine.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::OBOterm:
file: Bio/Ontology/OBOterm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::Ontology:
file: Bio/Ontology/Ontology.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::OntologyEngineI:
file: Bio/Ontology/OntologyEngineI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::OntologyI:
file: Bio/Ontology/OntologyI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::OntologyStore:
file: Bio/Ontology/OntologyStore.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::Path:
file: Bio/Ontology/Path.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::PathI:
file: Bio/Ontology/PathI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::Relationship:
file: Bio/Ontology/Relationship.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::RelationshipFactory:
file: Bio/Ontology/RelationshipFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::RelationshipI:
file: Bio/Ontology/RelationshipI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::RelationshipType:
file: Bio/Ontology/RelationshipType.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::SimpleGOEngine::GraphAdaptor:
file: Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::SimpleOntologyEngine:
file: Bio/Ontology/SimpleOntologyEngine.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::Term:
file: Bio/Ontology/Term.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::TermFactory:
file: Bio/Ontology/TermFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Ontology::TermI:
file: Bio/Ontology/TermI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO:
file: Bio/OntologyIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::Handlers::BaseSAXHandler:
file: Bio/OntologyIO/Handlers/BaseSAXHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::Handlers::InterProHandler:
file: Bio/OntologyIO/Handlers/InterProHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler:
file: Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::InterProParser:
file: Bio/OntologyIO/InterProParser.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::dagflat:
file: Bio/OntologyIO/dagflat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::goflat:
file: Bio/OntologyIO/goflat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::obo:
file: Bio/OntologyIO/obo.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::simplehierarchy:
file: Bio/OntologyIO/simplehierarchy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::OntologyIO::soflat:
file: Bio/OntologyIO/soflat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::ParameterBaseI:
file: Bio/ParameterBaseI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Perl:
file: Bio/Perl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::Correlate:
file: Bio/Phenotype/Correlate.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::MeSH::Term:
file: Bio/Phenotype/MeSH/Term.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::MeSH::Twig:
file: Bio/Phenotype/MeSH/Twig.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::Measure:
file: Bio/Phenotype/Measure.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::OMIM::MiniMIMentry:
file: Bio/Phenotype/OMIM/MiniMIMentry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::OMIM::OMIMentry:
file: Bio/Phenotype/OMIM/OMIMentry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::OMIM::OMIMentryAllelicVariant:
file: Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::OMIM::OMIMparser:
file: Bio/Phenotype/OMIM/OMIMparser.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::Phenotype:
file: Bio/Phenotype/Phenotype.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Phenotype::PhenotypeI:
file: Bio/Phenotype/PhenotypeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork:
file: Bio/PhyloNetwork.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::Factory:
file: Bio/PhyloNetwork/Factory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::FactoryX:
file: Bio/PhyloNetwork/FactoryX.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::GraphViz:
file: Bio/PhyloNetwork/GraphViz.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::RandomFactory:
file: Bio/PhyloNetwork/RandomFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::TreeFactory:
file: Bio/PhyloNetwork/TreeFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::TreeFactoryMulti:
file: Bio/PhyloNetwork/TreeFactoryMulti.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::TreeFactoryX:
file: Bio/PhyloNetwork/TreeFactoryX.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PhyloNetwork::muVector:
file: Bio/PhyloNetwork/muVector.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Genotype:
file: Bio/PopGen/Genotype.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::GenotypeI:
file: Bio/PopGen/GenotypeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::HtSNP:
file: Bio/PopGen/HtSNP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IO:
file: Bio/PopGen/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IO::csv:
file: Bio/PopGen/IO/csv.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IO::hapmap:
file: Bio/PopGen/IO/hapmap.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IO::phase:
file: Bio/PopGen/IO/phase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IO::prettybase:
file: Bio/PopGen/IO/prettybase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Individual:
file: Bio/PopGen/Individual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::IndividualI:
file: Bio/PopGen/IndividualI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Marker:
file: Bio/PopGen/Marker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::MarkerI:
file: Bio/PopGen/MarkerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::PopStats:
file: Bio/PopGen/PopStats.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Population:
file: Bio/PopGen/Population.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::PopulationI:
file: Bio/PopGen/PopulationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Simulation::Coalescent:
file: Bio/PopGen/Simulation/Coalescent.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Simulation::GeneticDrift:
file: Bio/PopGen/Simulation/GeneticDrift.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Statistics:
file: Bio/PopGen/Statistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::TagHaplotype:
file: Bio/PopGen/TagHaplotype.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PopGen::Utilities:
file: Bio/PopGen/Utilities.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PrimarySeq:
file: Bio/PrimarySeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PrimarySeq::Fasta:
file: Bio/DB/Fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PrimarySeqI:
file: Bio/PrimarySeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::PullParserI:
file: Bio/PullParserI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Range:
file: Bio/Range.pm
- version: '1.007001'
+ version: '1.007002'
Bio::RangeI:
file: Bio/RangeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::Analysis:
file: Bio/Restriction/Analysis.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::Enzyme:
file: Bio/Restriction/Enzyme.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::Enzyme::MultiCut:
file: Bio/Restriction/Enzyme/MultiCut.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::Enzyme::MultiSite:
file: Bio/Restriction/Enzyme/MultiSite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::EnzymeCollection:
file: Bio/Restriction/EnzymeCollection.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::EnzymeI:
file: Bio/Restriction/EnzymeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO:
file: Bio/Restriction/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO::bairoch:
file: Bio/Restriction/IO/bairoch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO::base:
file: Bio/Restriction/IO/base.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO::itype2:
file: Bio/Restriction/IO/itype2.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO::prototype:
file: Bio/Restriction/IO/prototype.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Restriction::IO::withrefm:
file: Bio/Restriction/IO/withrefm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Build:
file: Bio/Root/Build.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Exception:
file: Bio/Root/Exception.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::HTTPget:
file: Bio/Root/HTTPget.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::IO:
file: Bio/Root/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Root:
file: Bio/Root/Root.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::RootI:
file: Bio/Root/RootI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Storable:
file: Bio/Root/Storable.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Test:
file: Bio/Root/Test.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::TestObject:
file: Bio/Root/TestObject.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Utilities:
file: Bio/Root/Utilities.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Root::Version:
file: Bio/Root/Version.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::BlastStatistics:
file: Bio/Search/BlastStatistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::BlastUtils:
file: Bio/Search/BlastUtils.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::DatabaseI:
file: Bio/Search/DatabaseI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::GenericDatabase:
file: Bio/Search/GenericDatabase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::GenericStatistics:
file: Bio/Search/GenericStatistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::BlastHSP:
file: Bio/Search/HSP/BlastHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::BlastPullHSP:
file: Bio/Search/HSP/BlastPullHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::FastaHSP:
file: Bio/Search/HSP/FastaHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::GenericHSP:
file: Bio/Search/HSP/GenericHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::HMMERHSP:
file: Bio/Search/HSP/HMMERHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::HSPFactory:
file: Bio/Search/HSP/HSPFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::HSPI:
- file: Bio/Search/Tiling/MapTileUtils.pm
- version: '1.007001'
+ file: Bio/Search/HSP/HSPI.pm
+ version: '1.007002'
Bio::Search::HSP::HmmpfamHSP:
file: Bio/Search/HSP/HmmpfamHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::ModelHSP:
file: Bio/Search/HSP/ModelHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::PSLHSP:
file: Bio/Search/HSP/PSLHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::PsiBlastHSP:
file: Bio/Search/HSP/PsiBlastHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::PullHSPI:
file: Bio/Search/HSP/PullHSPI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::HSP::WABAHSP:
file: Bio/Search/HSP/WABAHSP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::BlastHit:
file: Bio/Search/Hit/BlastHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::BlastPullHit:
file: Bio/Search/Hit/BlastPullHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::Fasta:
file: Bio/Search/Hit/Fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::GenericHit:
file: Bio/Search/Hit/GenericHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::HMMERHit:
file: Bio/Search/Hit/HMMERHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::HitFactory:
file: Bio/Search/Hit/HitFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::HitI:
file: Bio/Search/Hit/HitI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::HmmpfamHit:
file: Bio/Search/Hit/HmmpfamHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::ModelHit:
file: Bio/Search/Hit/ModelHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::PsiBlastHit:
file: Bio/Search/Hit/PsiBlastHit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::PullHitI:
file: Bio/Search/Hit/PullHitI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Hit::hmmer3Hit:
file: Bio/Search/Hit/hmmer3Hit.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Iteration::GenericIteration:
file: Bio/Search/Iteration/GenericIteration.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Iteration::IterationI:
file: Bio/Search/Iteration/IterationI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Processor:
file: Bio/Search/Processor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::BlastPullResult:
file: Bio/Search/Result/BlastPullResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::BlastResult:
file: Bio/Search/Result/BlastResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::CrossMatchResult:
file: Bio/Search/Result/CrossMatchResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::GenericResult:
file: Bio/Search/Result/GenericResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::HMMERResult:
file: Bio/Search/Result/HMMERResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::HmmpfamResult:
file: Bio/Search/Result/HmmpfamResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::INFERNALResult:
file: Bio/Search/Result/INFERNALResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::PullResultI:
file: Bio/Search/Result/PullResultI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::ResultFactory:
file: Bio/Search/Result/ResultFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::ResultI:
file: Bio/Search/Result/ResultI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::WABAResult:
file: Bio/Search/Result/WABAResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Result::hmmer3Result:
file: Bio/Search/Result/hmmer3Result.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::SearchUtils:
file: Bio/Search/SearchUtils.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::StatisticsI:
file: Bio/Search/StatisticsI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Tiling::MapTileUtils:
file: Bio/Search/Tiling/MapTileUtils.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Tiling::MapTiling:
file: Bio/Search/Tiling/MapTiling.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Search::Tiling::TilingI:
file: Bio/Search/Tiling/TilingI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchDist:
file: Bio/SearchDist.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO:
file: Bio/SearchIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::EventHandlerI:
file: Bio/SearchIO/EventHandlerI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::FastHitEventBuilder:
file: Bio/SearchIO/FastHitEventBuilder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::IteratedSearchResultEventBuilder:
file: Bio/SearchIO/IteratedSearchResultEventBuilder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::SearchResultEventBuilder:
file: Bio/SearchIO/SearchResultEventBuilder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::SearchWriterI:
file: Bio/SearchIO/SearchWriterI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::GbrowseGFF:
file: Bio/SearchIO/Writer/GbrowseGFF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::HSPTableWriter:
file: Bio/SearchIO/Writer/HSPTableWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::HTMLResultWriter:
file: Bio/SearchIO/Writer/HTMLResultWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::HitTableWriter:
file: Bio/SearchIO/Writer/HitTableWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::ResultTableWriter:
file: Bio/SearchIO/Writer/ResultTableWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::Writer::TextResultWriter:
file: Bio/SearchIO/Writer/TextResultWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::axt:
file: Bio/SearchIO/axt.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::blast:
file: Bio/SearchIO/blast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::blast_pull:
file: Bio/SearchIO/blast_pull.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::blasttable:
file: Bio/SearchIO/blasttable.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::cross_match:
file: Bio/SearchIO/cross_match.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::erpin:
file: Bio/SearchIO/erpin.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::exonerate:
file: Bio/SearchIO/exonerate.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::fasta:
file: Bio/SearchIO/fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::gmap_f9:
file: Bio/SearchIO/gmap_f9.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::hmmer:
file: Bio/SearchIO/hmmer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::hmmer2:
file: Bio/SearchIO/hmmer2.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::hmmer3:
file: Bio/SearchIO/hmmer3.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::hmmer_pull:
file: Bio/SearchIO/hmmer_pull.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::infernal:
file: Bio/SearchIO/infernal.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::megablast:
file: Bio/SearchIO/megablast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::psl:
file: Bio/SearchIO/psl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::rnamotif:
file: Bio/SearchIO/rnamotif.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::sim4:
file: Bio/SearchIO/sim4.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::waba:
file: Bio/SearchIO/waba.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SearchIO::wise:
file: Bio/SearchIO/wise.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq:
file: Bio/Seq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::BaseSeqProcessor:
file: Bio/Seq/BaseSeqProcessor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::EncodedSeq:
file: Bio/Seq/EncodedSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::LargeLocatableSeq:
file: Bio/Seq/LargeLocatableSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::LargePrimarySeq:
file: Bio/Seq/LargePrimarySeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::LargeSeq:
file: Bio/Seq/LargeSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::LargeSeqI:
file: Bio/Seq/LargeSeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::Meta:
file: Bio/Seq/Meta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::Meta::Array:
file: Bio/Seq/Meta/Array.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::MetaI:
file: Bio/Seq/MetaI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::PrimaryQual:
file: Bio/Seq/PrimaryQual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::PrimaryQual::Qual:
file: Bio/DB/Qual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::PrimedSeq:
file: Bio/Seq/PrimedSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::QualI:
file: Bio/Seq/QualI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::Quality:
file: Bio/Seq/Quality.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::RichSeq:
file: Bio/Seq/RichSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::RichSeqI:
file: Bio/Seq/RichSeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SeqBuilder:
file: Bio/Seq/SeqBuilder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SeqFactory:
file: Bio/Seq/SeqFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SeqFastaSpeedFactory:
file: Bio/Seq/SeqFastaSpeedFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SeqWithQuality:
file: Bio/Seq/SeqWithQuality.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SequenceTrace:
file: Bio/Seq/SequenceTrace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::SimulatedRead:
file: Bio/Seq/SimulatedRead.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Seq::TraceI:
file: Bio/Seq/TraceI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqAnalysisParserI:
file: Bio/SeqAnalysisParserI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqEvolution::DNAPoint:
file: Bio/SeqEvolution/DNAPoint.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqEvolution::EvolutionI:
file: Bio/SeqEvolution/EvolutionI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqEvolution::Factory:
file: Bio/SeqEvolution/Factory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Amplicon:
file: Bio/SeqFeature/Amplicon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::AnnotationAdaptor:
file: Bio/SeqFeature/AnnotationAdaptor.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Collection:
file: Bio/SeqFeature/Collection.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::CollectionI:
file: Bio/SeqFeature/CollectionI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Computation:
file: Bio/SeqFeature/Computation.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::FeaturePair:
file: Bio/SeqFeature/FeaturePair.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::Exon:
file: Bio/SeqFeature/Gene/Exon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::ExonI:
file: Bio/SeqFeature/Gene/ExonI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::GeneStructure:
file: Bio/SeqFeature/Gene/GeneStructure.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::GeneStructureI:
file: Bio/SeqFeature/Gene/GeneStructureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::Intron:
file: Bio/SeqFeature/Gene/Intron.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::NC_Feature:
file: Bio/SeqFeature/Gene/NC_Feature.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::Poly_A_site:
file: Bio/SeqFeature/Gene/Poly_A_site.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::Promoter:
file: Bio/SeqFeature/Gene/Promoter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::Transcript:
file: Bio/SeqFeature/Gene/Transcript.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::TranscriptI:
file: Bio/SeqFeature/Gene/TranscriptI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Gene::UTR:
file: Bio/SeqFeature/Gene/UTR.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Generic:
file: Bio/SeqFeature/Generic.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Lite:
file: Bio/SeqFeature/Lite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::PositionProxy:
file: Bio/SeqFeature/PositionProxy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Primer:
file: Bio/SeqFeature/Primer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::SiRNA::Oligo:
file: Bio/SeqFeature/SiRNA/Oligo.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::SiRNA::Pair:
file: Bio/SeqFeature/SiRNA/Pair.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Similarity:
file: Bio/SeqFeature/Similarity.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::SimilarityPair:
file: Bio/SeqFeature/SimilarityPair.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::SubSeq:
file: Bio/SeqFeature/SubSeq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Tools::FeatureNamer:
file: Bio/SeqFeature/Tools/FeatureNamer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Tools::IDHandler:
file: Bio/SeqFeature/Tools/IDHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Tools::TypeMapper:
file: Bio/SeqFeature/Tools/TypeMapper.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::Tools::Unflattener:
file: Bio/SeqFeature/Tools/Unflattener.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeature::TypedSeqFeatureI:
file: Bio/SeqFeature/TypedSeqFeatureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqFeatureI:
file: Bio/SeqFeatureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqI:
file: Bio/SeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO:
file: Bio/SeqIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::FTHelper:
file: Bio/SeqIO/FTHelper.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::Handler::GenericRichSeqHandler:
file: Bio/SeqIO/Handler/GenericRichSeqHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::MultiFile:
file: Bio/SeqIO/MultiFile.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::abi:
file: Bio/SeqIO/abi.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::ace:
file: Bio/SeqIO/ace.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::agave:
file: Bio/SeqIO/agave.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::alf:
file: Bio/SeqIO/alf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::asciitree:
file: Bio/SeqIO/asciitree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::bsml:
file: Bio/SeqIO/bsml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::bsml_sax:
file: Bio/SeqIO/bsml_sax.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::chadoxml:
file: Bio/SeqIO/chadoxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::chaos:
file: Bio/SeqIO/chaos.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::chaosxml:
file: Bio/SeqIO/chaosxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::ctf:
file: Bio/SeqIO/ctf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::embl:
file: Bio/SeqIO/embl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::embldriver:
file: Bio/SeqIO/embldriver.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::entrezgene:
file: Bio/SeqIO/entrezgene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::excel:
file: Bio/SeqIO/excel.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::exp:
file: Bio/SeqIO/exp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::fasta:
file: Bio/SeqIO/fasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::fastq:
file: Bio/SeqIO/fastq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::flybase_chadoxml:
file: Bio/SeqIO/flybase_chadoxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game:
file: Bio/SeqIO/game.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game::featHandler:
file: Bio/SeqIO/game/featHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game::gameHandler:
file: Bio/SeqIO/game/gameHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game::gameSubs:
file: Bio/SeqIO/game/gameSubs.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game::gameWriter:
file: Bio/SeqIO/game/gameWriter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::game::seqHandler:
file: Bio/SeqIO/game/seqHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::gbdriver:
file: Bio/SeqIO/gbdriver.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::gbxml:
file: Bio/SeqIO/gbxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::gcg:
file: Bio/SeqIO/gcg.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::genbank:
file: Bio/SeqIO/genbank.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::interpro:
file: Bio/SeqIO/interpro.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::kegg:
file: Bio/SeqIO/kegg.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::largefasta:
file: Bio/SeqIO/largefasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::lasergene:
file: Bio/SeqIO/lasergene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::locuslink:
file: Bio/SeqIO/locuslink.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::mbsout:
file: Bio/SeqIO/mbsout.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::metafasta:
file: Bio/SeqIO/metafasta.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::msout:
file: Bio/SeqIO/msout.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::nexml:
file: Bio/SeqIO/nexml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::phd:
file: Bio/SeqIO/phd.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::pir:
file: Bio/SeqIO/pir.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::pln:
file: Bio/SeqIO/pln.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::qual:
file: Bio/SeqIO/qual.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::raw:
file: Bio/SeqIO/raw.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::scf:
file: Bio/SeqIO/scf.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::seqxml:
file: Bio/SeqIO/seqxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::strider:
file: Bio/SeqIO/strider.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::swiss:
file: Bio/SeqIO/swiss.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::swissdriver:
file: Bio/SeqIO/swissdriver.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::tab:
file: Bio/SeqIO/tab.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::table:
file: Bio/SeqIO/table.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::tigr:
file: Bio/SeqIO/tigr.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::tigrxml:
file: Bio/SeqIO/tigrxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::tinyseq:
file: Bio/SeqIO/tinyseq.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::tinyseq::tinyseqHandler:
file: Bio/SeqIO/tinyseq/tinyseqHandler.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqIO::ztr:
file: Bio/SeqIO/ztr.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SeqUtils:
file: Bio/SeqUtils.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SimpleAlign:
file: Bio/SimpleAlign.pm
- version: '1.007001'
+ version: '1.007002'
Bio::SimpleAnalysisI:
file: Bio/SimpleAnalysisI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Species:
file: Bio/Species.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::Atom:
file: Bio/Structure/Atom.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::Chain:
file: Bio/Structure/Chain.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::Entry:
file: Bio/Structure/Entry.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::IO:
file: Bio/Structure/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::IO::pdb:
file: Bio/Structure/IO/pdb.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::Model:
file: Bio/Structure/Model.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::Residue:
file: Bio/Structure/Residue.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::SecStr::DSSP::Res:
file: Bio/Structure/SecStr/DSSP/Res.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::SecStr::STRIDE::Res:
file: Bio/Structure/SecStr/STRIDE/Res.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Structure::StructureI:
file: Bio/Structure/StructureI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::Alphabet:
file: Bio/Symbol/Alphabet.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::AlphabetI:
file: Bio/Symbol/AlphabetI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::DNAAlphabet:
file: Bio/Symbol/DNAAlphabet.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::ProteinAlphabet:
file: Bio/Symbol/ProteinAlphabet.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::Symbol:
file: Bio/Symbol/Symbol.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Symbol::SymbolI:
file: Bio/Symbol/SymbolI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxon:
file: Bio/Taxon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxonomy:
file: Bio/Taxonomy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxonomy::FactoryI:
file: Bio/Taxonomy/FactoryI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxonomy::Node:
file: Bio/Taxonomy/Node.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxonomy::Taxon:
file: Bio/Taxonomy/Taxon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Taxonomy::Tree:
file: Bio/Taxonomy/Tree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::AlignFactory:
file: Bio/Tools/AlignFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Alignment::Consed:
file: Bio/Tools/Alignment/Consed.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Alignment::Trim:
file: Bio/Tools/Alignment/Trim.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::AmpliconSearch:
file: Bio/Tools/AmpliconSearch.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::DNA::ESEfinder:
file: Bio/Tools/Analysis/DNA/ESEfinder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::Domcut:
file: Bio/Tools/Analysis/Protein/Domcut.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::ELM:
file: Bio/Tools/Analysis/Protein/ELM.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::GOR4:
file: Bio/Tools/Analysis/Protein/GOR4.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::HNN:
file: Bio/Tools/Analysis/Protein/HNN.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::NetPhos:
file: Bio/Tools/Analysis/Protein/NetPhos.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::Scansite:
file: Bio/Tools/Analysis/Protein/Scansite.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::Protein::Sopma:
file: Bio/Tools/Analysis/Protein/Sopma.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Analysis::SimpleAnalysisBase:
file: Bio/Tools/Analysis/SimpleAnalysisBase.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::AnalysisResult:
file: Bio/Tools/AnalysisResult.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Blat:
file: Bio/Tools/Blat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::CodonTable:
file: Bio/Tools/CodonTable.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Coil:
file: Bio/Tools/Coil.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::ECnumber:
file: Bio/Tools/ECnumber.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::EMBOSS::Palindrome:
file: Bio/Tools/EMBOSS/Palindrome.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::EPCR:
file: Bio/Tools/EPCR.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::ESTScan:
file: Bio/Tools/ESTScan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Eponine:
file: Bio/Tools/Eponine.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Est2Genome:
file: Bio/Tools/Est2Genome.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Fgenesh:
file: Bio/Tools/Fgenesh.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::FootPrinter:
file: Bio/Tools/FootPrinter.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::GFF:
file: Bio/Tools/GFF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Gel:
file: Bio/Tools/Gel.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Geneid:
file: Bio/Tools/Geneid.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Genemark:
file: Bio/Tools/Genemark.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Genewise:
file: Bio/Tools/Genewise.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Genomewise:
file: Bio/Tools/Genomewise.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Genscan:
file: Bio/Tools/Genscan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Glimmer:
file: Bio/Tools/Glimmer.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Grail:
file: Bio/Tools/Grail.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::GuessSeqFormat:
file: Bio/Tools/GuessSeqFormat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::HMMER::Domain:
file: Bio/Tools/HMMER/Domain.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::HMMER::Results:
file: Bio/Tools/HMMER/Results.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::HMMER::Set:
file: Bio/Tools/HMMER/Set.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Hmmpfam:
file: Bio/Tools/Hmmpfam.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::IUPAC:
file: Bio/Tools/IUPAC.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Lucy:
file: Bio/Tools/Lucy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::MZEF:
file: Bio/Tools/MZEF.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Match:
file: Bio/Tools/Match.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::OddCodes:
file: Bio/Tools/OddCodes.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Phylo::Gerp:
file: Bio/Tools/Phylo/Gerp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Phylo::Gumby:
file: Bio/Tools/Phylo/Gumby.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Phylo::Molphy:
file: Bio/Tools/Phylo/Molphy.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Phylo::Molphy::Result:
file: Bio/Tools/Phylo/Molphy/Result.pm
- version: '1.007001'
- Bio::Tools::Phylo::PAML:
- file: Bio/Tools/Phylo/PAML.pm
- version: '1.007001'
- Bio::Tools::Phylo::PAML::Codeml:
- file: Bio/Tools/Phylo/PAML/Codeml.pm
- version: '1.007001'
- Bio::Tools::Phylo::PAML::ModelResult:
- file: Bio/Tools/Phylo/PAML/ModelResult.pm
- version: '1.007001'
- Bio::Tools::Phylo::PAML::Result:
- file: Bio/Tools/Phylo/PAML/Result.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Phylo::Phylip::ProtDist:
file: Bio/Tools/Phylo/Phylip/ProtDist.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Prediction::Exon:
file: Bio/Tools/Prediction/Exon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Prediction::Gene:
file: Bio/Tools/Prediction/Gene.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Primer3:
file: Bio/Tools/Primer3.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Primer::Assessor::Base:
file: Bio/Tools/Primer/Assessor/Base.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Primer::AssessorI:
file: Bio/Tools/Primer/AssessorI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Primer::Feature:
file: Bio/Tools/Primer/Feature.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Primer::Pair:
file: Bio/Tools/Primer/Pair.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Prints:
file: Bio/Tools/Prints.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Profile:
file: Bio/Tools/Profile.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Promoterwise:
file: Bio/Tools/Promoterwise.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::PrositeScan:
file: Bio/Tools/PrositeScan.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Protparam:
file: Bio/Tools/Protparam.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Pseudowise:
file: Bio/Tools/Pseudowise.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::QRNA:
file: Bio/Tools/QRNA.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::RandomDistFunctions:
file: Bio/Tools/RandomDistFunctions.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::RepeatMasker:
file: Bio/Tools/RepeatMasker.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Run::GenericParameters:
file: Bio/Tools/Run/GenericParameters.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Run::ParametersI:
file: Bio/Tools/Run/ParametersI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Run::RemoteBlast:
file: Bio/Tools/Run/RemoteBlast.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Seg:
file: Bio/Tools/Seg.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SeqPattern:
file: Bio/Tools/SeqPattern.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SeqPattern::Backtranslate:
file: Bio/Tools/SeqPattern/Backtranslate.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SeqStats:
file: Bio/Tools/SeqStats.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SeqWords:
file: Bio/Tools/SeqWords.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SiRNA:
file: Bio/Tools/SiRNA.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SiRNA::Ruleset::saigo:
file: Bio/Tools/SiRNA/Ruleset/saigo.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::SiRNA::Ruleset::tuschl:
file: Bio/Tools/SiRNA/Ruleset/tuschl.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Sigcleave:
file: Bio/Tools/Sigcleave.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Signalp:
file: Bio/Tools/Signalp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Signalp::ExtendedSignalp:
file: Bio/Tools/Signalp/ExtendedSignalp.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Sim4::Exon:
file: Bio/Tools/Sim4/Exon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Sim4::Results:
file: Bio/Tools/Sim4/Results.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Spidey::Exon:
file: Bio/Tools/Spidey/Exon.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Spidey::Results:
file: Bio/Tools/Spidey/Results.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::TandemRepeatsFinder:
file: Bio/Tools/TandemRepeatsFinder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::TargetP:
file: Bio/Tools/TargetP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::Tmhmm:
file: Bio/Tools/Tmhmm.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::dpAlign:
file: Bio/Tools/dpAlign.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::ipcress:
file: Bio/Tools/ipcress.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::isPcr:
file: Bio/Tools/isPcr.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::pICalculator:
file: Bio/Tools/pICalculator.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::pSW:
file: Bio/Tools/pSW.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tools::tRNAscanSE:
file: Bio/Tools/tRNAscanSE.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::AlleleNode:
file: Bio/Tree/AlleleNode.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::AnnotatableNode:
file: Bio/Tree/AnnotatableNode.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::Compatible:
file: Bio/Tree/Compatible.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::DistanceFactory:
file: Bio/Tree/DistanceFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::Draw::Cladogram:
file: Bio/Tree/Draw/Cladogram.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::Node:
file: Bio/Tree/Node.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::NodeI:
file: Bio/Tree/NodeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::NodeNHX:
file: Bio/Tree/NodeNHX.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::RandomFactory:
file: Bio/Tree/RandomFactory.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::Statistics:
file: Bio/Tree/Statistics.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::Tree:
file: Bio/Tree/Tree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::TreeFunctionsI:
file: Bio/Tree/TreeFunctionsI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Tree::TreeI:
file: Bio/Tree/TreeI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO:
file: Bio/TreeIO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::NewickParser:
file: Bio/TreeIO/NewickParser.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::TreeEventBuilder:
file: Bio/TreeIO/TreeEventBuilder.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::cluster:
file: Bio/TreeIO/cluster.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::lintree:
file: Bio/TreeIO/lintree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::newick:
file: Bio/TreeIO/newick.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::nexml:
file: Bio/TreeIO/nexml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::nexus:
file: Bio/TreeIO/nexus.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::nhx:
file: Bio/TreeIO/nhx.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::pag:
file: Bio/TreeIO/pag.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::phyloxml:
file: Bio/TreeIO/phyloxml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::svggraph:
file: Bio/TreeIO/svggraph.pm
- version: '1.007001'
+ version: '1.007002'
Bio::TreeIO::tabtree:
file: Bio/TreeIO/tabtree.pm
- version: '1.007001'
+ version: '1.007002'
Bio::UpdateableSeqI:
file: Bio/UpdateableSeqI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::AAChange:
file: Bio/Variation/AAChange.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::AAReverseMutate:
file: Bio/Variation/AAReverseMutate.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::Allele:
file: Bio/Variation/Allele.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::DNAMutation:
file: Bio/Variation/DNAMutation.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::IO:
file: Bio/Variation/IO.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::IO::flat:
file: Bio/Variation/IO/flat.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::IO::xml:
file: Bio/Variation/IO/xml.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::RNAChange:
file: Bio/Variation/RNAChange.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::SNP:
file: Bio/Variation/SNP.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::SeqDiff:
file: Bio/Variation/SeqDiff.pm
- version: '1.007001'
+ version: '1.007002'
Bio::Variation::VariantI:
file: Bio/Variation/VariantI.pm
- version: '1.007001'
+ version: '1.007002'
Bio::WebAgent:
file: Bio/WebAgent.pm
- version: '1.007001'
+ version: '1.007002'
FeatureStore:
file: Bio/DB/GFF/Adaptor/berkeleydb.pm
- version: '1.007001'
+ version: '1.007002'
recommends:
Algorithm::Munkres: '0'
Array::Compare: '0'
@@ -2474,4 +2462,5 @@ requires:
perl: v5.6.1
resources:
license: http://dev.perl.org/licenses/
-version: '1.007001'
+version: '1.007002'
+x_serialization_backend: 'CPAN::Meta::YAML version 0.018'
diff --git a/deobfuscator/Deobfuscator/bin/deob_index.pl b/deobfuscator/Deobfuscator/bin/deob_index.pl
index c5fcd4b..b7a3e2d 100755
--- a/deobfuscator/Deobfuscator/bin/deob_index.pl
+++ b/deobfuscator/Deobfuscator/bin/deob_index.pl
@@ -48,9 +48,9 @@ for details.
While going through and trying to parse each module, deob_index.pl also
reports what pieces of the documentation it can't find. For example, if
-a method's documentation doesn't describe the data type it returns, this
+a method's documentation doesn't describe the data type it returns, this
script logs that information to a file. This type of automated documentation-
-checking could be used to standardize and improve the documentation in
+checking could be used to standardize and improve the documentation in
BioPerl.
deob_index.pl creates four files:
@@ -67,20 +67,20 @@ This file is used by L<deob_interface.cgi>.
A Berkeley DB, which stores package-level documentation, such as
the synopsis and the description. Each key is a package name,
-e.g. "Bio::SeqIO", and each value string is composed of the
-individual pieces of the documentation kept separate by
-unique string record separators. The individual pieces of
-documentation are pulled out of the string using the
+e.g. "Bio::SeqIO", and each value string is composed of the
+individual pieces of the documentation kept separate by
+unique string record separators. The individual pieces of
+documentation are pulled out of the string using the
get_pkg_docs function in Deobfuscator.pm. See that package
for details.
=item C<< methods.db >>
-Like packages.db, methods.db is also a Berkeley DB, except it
+Like packages.db, methods.db is also a Berkeley DB, except it
stores various pieces of information about individual methods
available to a class. Each method might have documentation
about its usage, its arguments, its return values, an example,
-and a description of its function.
+and a description of its function.
Each key is the fully-qualified method name, e.g.
"Bio::SeqIO::next_seq". Each value is a string containing all
@@ -184,7 +184,7 @@ This software requires:
=item A working installation of the Berkeley DB
-The Berkeley DB comes standard with most UNIX distributions, so you may
+The Berkeley DB comes standard with most UNIX distributions, so you may
already have it installed. See L<http://www.sleepycat.com> for more information.
=item BioPerl
@@ -222,7 +222,7 @@ will cause deob_index.pl to report them as errors. Although the consistency
of this standard is desirable for end-users of the documentation, this code
probably needs to be a little bit more flexible (patches welcome!).
-This software has only been tested in a UNIX environment.
+This software has only been tested in a UNIX environment.
=head1 FEEDBACK
@@ -234,7 +234,7 @@ Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
=head2 Reporting Bugs
@@ -308,12 +308,12 @@ and stores the info in a database.
USAGE: deob_index.pl [-s bioperl-version] [-x exclude_file] <BioPerl lib dir> <output dir>
-where
+where
<BioPerl lib dir> is the BioPerl distribution you'd like to index
e.g. /export/share/lib/perl5/site_perl/5.8.7/Bio/
-
+
and
<output dir> is where the output files should be placed
@@ -385,7 +385,7 @@ my %FLAG;
$pkg_db->{'__BioPerl_Version'} = $opt_s ? $opt_s : 'unknown';
# keep stats on our indexing
-my %stats = (
+my %stats = (
'files' => 0,
'pkg_name' => 0,
'desc' => 0,
@@ -429,7 +429,7 @@ chmod($mode, $pkg_file, $meth_file, $list_file);
sub extract_pod {
my ($file) = $_;
my $long_file = $File::Find::name;
-
+
# skip if it's on our exclude list
foreach my $one (keys %exclude) {
if ($File::Find::name =~ /$one$/) {
diff --git a/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi b/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
index 301c60d..4e7c4a2 100644
--- a/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
+++ b/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
@@ -71,7 +71,7 @@ Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
=head2 Reporting Bugs
diff --git a/deobfuscator/Deobfuscator/cgi-bin/deob_help.html b/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
index a379b62..e86dba1 100644
--- a/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
+++ b/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
@@ -5,7 +5,7 @@
<p>The Deobfuscator was written to make it easier to determine the methods that
are available from a given BioPerl module.</p>
<p>BioPerl is a highly object-oriented software package, with often multiple
-levels of inheritance. Although each individual module is usually well
+levels of inheritance. Although each individual module is usually well
documented for the methods specific to it, identifying the inherited methods
is less straightforward.</p>
<p>The Deobfuscator indexes all of the BioPerl POD documentation, taking account
@@ -23,7 +23,7 @@ of the Bioperl mailing lists. Your participation is much appreciated.</p>
<ul>
<li><a href="mailto:bioperl-l at bioperl.org">General discussion</a>
-<li><a href="http://www.bioperl.org/wiki/Mailing_lists">About the mailing lists</a>
+<li><a href="http://bioperl.org/Support.html">About the mailing lists</a>
</ul>
<h3>Reporting Bugs</h3>
<p>Report bugs to the Bioperl bug tracking system to help us keep track
diff --git a/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi b/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
index da1c0a4..c373ace 100755
--- a/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
+++ b/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
@@ -150,7 +150,7 @@ Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
=head2 Reporting Bugs
@@ -317,7 +317,7 @@ print <<CSHL;
<br>
<br>
<div>
- <form name="searchForm" action="">
+ <form name="searchForm" action="">
<input type="hidden" name="Search">
<input type="hidden" name="module">
<input type="hidden" name="sort_order" value="$sort_order">
diff --git a/deobfuscator/Deobfuscator/lib/Deobfuscator.pm b/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
index d66816a..2ed4aad 100644
--- a/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
+++ b/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
@@ -82,7 +82,7 @@ files aren't in the correct place.
=item C<< error: couldn't close database >>
-One of the Berkeley databases couldn't be closed. This might just be a
+One of the Berkeley databases couldn't be closed. This might just be a
transient filesystem error.
=back
@@ -105,7 +105,7 @@ This software requires:
=item A working installation of the Berkeley DB
-The Berkeley DB comes standard with most UNIX distributions, so you may
+The Berkeley DB comes standard with most UNIX distributions, so you may
already have it installed. See L<http://www.sleepycat.com> for more information.
=item BioPerl
@@ -146,7 +146,7 @@ Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
- http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
+ http://bioperl.org/Support.html - About the mailing lists
=head2 Reporting Bugs
@@ -225,7 +225,7 @@ Function: traverses the inheritance tree for a given class to determine
Returns : a reference to a hash. The hash keys are fully-qualified class
names, such as 'Bio::SeqIO'. The hash values are references to
- an array of hashes, where each array element is a reference to
+ an array of hashes, where each array element is a reference to
a hash containing two key-value pairs, 'method' and 'class';
Args : a list of fully-qualified class names
@@ -334,7 +334,7 @@ sub _load_module {
my $module = shift;
eval "require $module";
my $err = $@ || 'eval returned undef';
-
+
if ($@) { return $@ }
else { return }
}
@@ -351,12 +351,12 @@ Args : a filename as a scalar
sub open_db {
my ($filename) = @_;
-
+
my %hash;
my $hashref = \%hash;
-
+
tie %hash, "DB_File", $filename or die "error: couldn't open $filename: $!\n";
-
+
return $hashref;
}
@@ -372,7 +372,7 @@ Args : a hashref to a tied Berkeley DB
sub close_db {
my ($hashref) = @_;
-
+
untie $hashref or die "error: couldn't close database: $!\n";
}
@@ -396,7 +396,7 @@ sub get_pkg_docs {
# hash to store our hash value, now split out into its constituent parts
my %record;
-
+
my $rec_sep = 'DaVe-ReC-sEp';
# if the method isn't in our db
@@ -405,7 +405,7 @@ sub get_pkg_docs {
}
# grab the constituent parts of the pkg record
- ( $record{'short_desc'}, $record{'synopsis'}, $record{'desc'} ) =
+ ( $record{'short_desc'}, $record{'synopsis'}, $record{'desc'} ) =
( split $rec_sep, $db_hashref->{$pkg_name} );
# return just the part that was asked for
@@ -451,20 +451,20 @@ sub get_method_docs {
# put individual info types into separate hash entries...
foreach my $part (@parts) {
if ($part =~ /^-(\w+)\|(.*)/) { $record{$1} = $2; }
-
+
# ... and put the whole thing into one big string
$whole_record .= "$part\n";
}
# return a specific part if that was asked for
if ($info_type) {
- # return just the part that was asked for
+ # return just the part that was asked for
if ( exists( $record{$info_type} ) ) {
# if there's really nothing in there, say so.
if ( ( $record{$info_type} =~ /^[\s\n]*$/)
|| ( $record{$info_type} eq '') ) { return 0; }
- else {
+ else {
return $record{$info_type};
}
}
diff --git a/examples/searchio/blast_example.pl b/examples/searchio/blast_example.pl
index 5dafb11..99c8418 100755
--- a/examples/searchio/blast_example.pl
+++ b/examples/searchio/blast_example.pl
@@ -4,7 +4,7 @@
# For example, $hsp->get_aln will return a Bio::SimpleAlign object,
# not the alignment in a printable form.
# This script was used to create the table in the SearchIO HOWTO,
-# found at http://bioperl.open-bio.org/wiki/HOWTO:SearchIO
+# found at http://bioperl.org/howtos/SearchIO_HOWTO.html
# Brian Osborne
use strict;
@@ -60,7 +60,7 @@ while ( my $result = $in->next_result ) {
print "Hit\tnum_hsps\t" . $hit->num_hsps . "\n";
print "Hit\tambiguous_aln\t" . $hit->ambiguous_aln . "\n";
print "Hit\toverlap\t" . $hit->overlap . "\n";
- print "Hit\tn\t" . $hit->n . "\n";
+ print "Hit\tn\t" . $hit->n . "\n";
print "Hit\tlogical_length\t" . $hit->logical_length . "\n";
print "Hit\tlength_aln\t" . $hit->length_aln . "\n";
print "Hit\tgaps\t" . $hit->gaps . "\n";
diff --git a/scripts/DB/bp_flanks.pl b/scripts/DB/bp_flanks.pl
index da92d1d..0f1415f 100644
--- a/scripts/DB/bp_flanks.pl
+++ b/scripts/DB/bp_flanks.pl
@@ -246,7 +246,7 @@ sequence the subsequence was taken.
The ID of the fasta entry is the name given at the command line joined
by hyphen to the filename or accesion of the source sequence. If no id
-is given a series of consequtive integers is used.
+is given a series of consecutive integers is used.
The tag=value pairs are:
diff --git a/scripts/index/bp_fetch.pl b/scripts/index/bp_fetch.pl
index b571616..86a5bbc 100644
--- a/scripts/index/bp_fetch.pl
+++ b/scripts/index/bp_fetch.pl
@@ -50,7 +50,7 @@ db information
options only for expert use
-dir <dir> - directory to find the index files
- (overrides BIOPERL_INDEX environment varaible)
+ (overrides BIOPERL_INDEX environment variable)
-type <type> - type of DBM file to open
(overrides BIOPERL_INDEX_TYPE environment variable)
@@ -163,7 +163,7 @@ BEGIN {
if ( $@ ) {
if ( !exists $ENV{'BIOPERL_SAVVY'} ) {
- print STDERR ("\nbp_fetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules\nThis is most likely because LWP has not been installed\nThis does not effect local indexing\nset environment variable BIOPERL_SAVVY to supress this message\n\n");
+ print STDERR ("\nbp_fetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules\nThis is most likely because LWP has not been installed\nThis does not effect local indexing\nset environment variable BIOPERL_SAVVY to suppress this message\n\n");
}
}
}
@@ -264,7 +264,7 @@ for my $arg ( @ARGV ) {
};
/^local$/ && do {
if ( !$dir ) {
- die "\nNo directory specified for index\nDirectory must be specified by the environment varaible BIOPERL_INDEX or --dir option\ngo bp_index with no arguments for more help\n\n";
+ die "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or --dir option\ngo bp_index with no arguments for more help\n\n";
}
#
diff --git a/scripts/index/bp_index.pl b/scripts/index/bp_index.pl
index b636da0..3af1e22 100644
--- a/scripts/index/bp_index.pl
+++ b/scripts/index/bp_index.pl
@@ -48,7 +48,7 @@ Options for expert use
=head1 ENVIRONMENT
bp_index and bp_fetch coordinate where the databases lie using the
-enviroment variable BIOPERL_INDEX. This can be overridden using the
+environment variable BIOPERL_INDEX. This can be overridden using the
-dir option. There is no default value, so you must use the -dir option
or set BIOPERL_INDEX.
@@ -143,7 +143,7 @@ exec('perldoc',$0) unless @ARGV;
my $name = shift;
if( !$dir ) {
- print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment varaible BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n";
+ print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n";
exit(1);
}
diff --git a/scripts/seq/bp_seqcut.pl b/scripts/seq/bp_seqcut.pl
index 401e0fb..789f15c 100644
--- a/scripts/seq/bp_seqcut.pl
+++ b/scripts/seq/bp_seqcut.pl
@@ -2,7 +2,7 @@
=head1 NAME
-I<bp_seqcut.pl>
+bp_seqcut.pl - cut FASTA sequences with a given range
=head1 USAGE
diff --git a/scripts/seq/bp_unflatten_seq.pl b/scripts/seq/bp_unflatten_seq.pl
index 730a111..4bbebc7 100644
--- a/scripts/seq/bp_unflatten_seq.pl
+++ b/scripts/seq/bp_unflatten_seq.pl
@@ -88,7 +88,7 @@ input file (can also be specified as last argument)
input format (defaults to genbank)
-probably doesnt make so much sense to use this for non-flat formats;
+probably doesn't make so much sense to use this for non-flat formats;
ie other than embl/genbank
=item -to FORMAT
diff --git a/scripts/utilities/bp_netinstall.pl b/scripts/utilities/bp_netinstall.pl
index 3d49947..0b539b8 100644
--- a/scripts/utilities/bp_netinstall.pl
+++ b/scripts/utilities/bp_netinstall.pl
@@ -2,7 +2,7 @@
=head1 NAME
-bp_netinstall.pl
+bp_netinstall.pl - Net-based installer of BioPerl
=head1 SYNOPSIS
diff --git a/scripts/utilities/bp_pairwise_kaks.pl b/scripts/utilities/bp_pairwise_kaks.pl
deleted file mode 100644
index 0a05a87..0000000
--- a/scripts/utilities/bp_pairwise_kaks.pl
+++ /dev/null
@@ -1,211 +0,0 @@
-#!perl
-use strict;
-use warnings;
-# Author Jason Stajich <jason-at-bioperl-dot-org>
-
-=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 at 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/scripts/utilities/bp_search2gff.pl b/scripts/utilities/bp_search2gff.pl
index c91cbd3..5079197 100644
--- a/scripts/utilities/bp_search2gff.pl
+++ b/scripts/utilities/bp_search2gff.pl
@@ -2,7 +2,7 @@
=head1 NAME
-bp_search2gff
+bp_search2gff - turn a SearchIO report into GFF
=head1 SYNOPSIS
diff --git a/t/LocalDB/Flat.t b/t/LocalDB/Flat.t
index 25174a6..7d8a673 100644
--- a/t/LocalDB/Flat.t
+++ b/t/LocalDB/Flat.t
@@ -7,7 +7,7 @@ BEGIN {
use lib '.';
use Bio::Root::Test;
- test_begin(-tests => 25,
+ test_begin(-tests => 27,
-requires_module => 'DB_File');
use_ok('Bio::DB::Flat');
@@ -59,7 +59,6 @@ $seq = $db->get_Seq_by_acc('CH236947.1');
ok($seq && ref($seq));
is($seq->length,192);
-
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
@@ -70,12 +69,16 @@ $db = Bio::DB::Flat->new(-directory => $tmpdir,
-write_flag => 1
);
-$dir= test_input_file('dbfa', '1.fa');
+$dir = test_input_file('dbfa', '1.fa');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('AW057119');
ok($seq);
-is($seq->length,808);
+is($seq->length, 808);
+$seq = $db->get_Seq_by_id('AW057118');
+ok($seq);
+is($seq->length, 299);
+
undef $db;
SKIP: {
diff --git a/t/RemoteDB/SeqVersion.t b/t/RemoteDB/SeqVersion.t
index 327a621..a43b21b 100644
--- a/t/RemoteDB/SeqVersion.t
+++ b/t/RemoteDB/SeqVersion.t
@@ -22,7 +22,7 @@ SKIP: {
test_skip( -tests => 8, -requires_networking => 1 );
throws_ok { $query->get_history('DODGY_ID_WHICH_SHOULD_FAIL') }
- qr/ID likely does not exist/i, 'throw on bad ID';
+ qr/ID likely does not exist|No table found/i, 'throw on bad ID';
my $latest_gi = $query->get_recent(2);
is($latest_gi, 2, 'get_recent');
diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t
index 3a7ddcf..306c99d 100644
--- a/t/RemoteDB/Taxonomy.t
+++ b/t/RemoteDB/Taxonomy.t
@@ -1,5 +1,4 @@
# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
use strict;
@@ -8,7 +7,7 @@ BEGIN {
use Bio::Root::Test;
test_begin(
- -tests => 214,
+ -tests => 220,
-requires_modules => [qw(DB_File
LWP::UserAgent
XML::Twig )]
@@ -172,12 +171,14 @@ for my $db ($db_entrez, $db_flatfile) {
is_deeply \@ids, [200795, 32061];
$id = $db->get_taxonids('Chloroflexi (class)');
- $db eq $db_entrez ? is($id, undef) : is($id, 32061);
+ $db eq $db_entrez ? is($id, 'No hit') : is($id, 32061);
@ids = $db->get_taxonids('Rhodotorula');
- cmp_ok @ids, '>=' , 2;
+ cmp_ok @ids, '>=' , 1;
if ($db eq $db_entrez) {
- ok grep { $_ == 592558 } @ids;
+ diag(join(",", @ids));
+ # From NCBI: Taxid 592558 was merged into taxid 5533 on June 16, 2017
+ is( (grep { $_ == 592558 } @ids), 0, 'Value no longer found');
ok grep { $_ == 5533 } @ids;
} else {
# note the locally cached flatfile is out-of-date, but technically
@@ -452,18 +453,18 @@ SKIP: {
test_skip(-tests => 12, -requires_networking => 1);
my $db=Bio::DB::Taxonomy->new(-source=>"entrez");
-
+
my @taxa = qw(viruses Deltavirus unclassified plasmid);
-
+
for my $taxon (@taxa) {
test_taxid($db, $taxon);
}
-
+
sub test_taxid {
my ($db, $taxa) = @_;
my @taxonids = $db->get_taxonids($taxa);
cmp_ok(scalar(@taxonids), '>', 0, "Got IDs returned for $taxa:".join(',', @taxonids));
- my $taxon;
+ my $taxon;
lives_ok { $taxon = $db->get_taxon(-taxonid => pop @taxonids) } "IDs generates a Bio::Taxonomy::Node";
if (defined $taxon) {
like( $taxon->scientific_name, qr/$taxa/i, "Name returned matches $taxa");
@@ -472,3 +473,33 @@ SKIP: {
}
}
}
+
+# tests for #212
+SKIP: {
+ test_skip( -tests => 6, -requires_networking => 1 );
+
+ my $db = Bio::DB::Taxonomy->new( -source => "entrez" );
+
+ # String | What I expect | What I get
+ # ---------------------- | ------------- | ----------
+ # 'Lissotriton vulgaris' | 8324 | 8324
+ # 'Chlorella vulgaris' | 3077 | 3077
+ # 'Phygadeuon solidus' | 1763951 | 1763951
+ # 'Ovatus' | 666060 | 666060
+ # 'Phygadeuon ovatus' | "No hit" | 666060
+ # 'Trimorus ovatus' | "No hit" | 666060
+
+ my @ids;
+ @ids = $db->get_taxonids('Lissotriton vulgaris');
+ is $ids[0], 8324, 'Correct: Lissotriton vulgaris';
+ @ids = $db->get_taxonids('Chlorella vulgaris');
+ is $ids[0], 3077, 'Correct: Chlorella vulgaris';
+ @ids = $db->get_taxonids('Phygadeuon solidus');
+ is $ids[0], 1763951, 'Correct: Phygadeuon solidus';
+ @ids = $db->get_taxonids('Ovatus');
+ is $ids[0], 666060, 'Correct: Ovatus';
+ @ids = $db->get_taxonids('Phygadeuon ovatus');
+ is $ids[0], 'No hit', 'Correct: No hit';
+ @ids = $db->get_taxonids('Trimorus ovatus');
+ is $ids[0], 'No hit', 'Correct: No hit';
+}
diff --git a/t/SeqIO/pir.t b/t/SeqIO/pir.t
index b7bfded..1b08769 100644
--- a/t/SeqIO/pir.t
+++ b/t/SeqIO/pir.t
@@ -1,30 +1,46 @@
# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
use strict;
BEGIN {
- use lib '.';
+ use lib '.';
use Bio::Root::Test;
-
- test_begin(-tests => 9);
-
- use_ok('Bio::SeqIO::pir');
+
+ test_begin( -tests => 12 );
+
+ use_ok('Bio::SeqIO::pir');
}
my $verbose = test_debug();
-my $str = Bio::SeqIO->new(-file => test_input_file('seqfile.pir'),
- -verbose => $verbose,
- -format => 'pir');
+my $in = Bio::SeqIO->new(
+ -file => test_input_file('seqfile.pir'),
+ -verbose => $verbose,
+ -format => 'pir'
+);
-ok ( defined $str, 'new instance is defined ');
-isa_ok ($str, 'Bio::SeqIO');
+ok( defined $in, 'new instance is defined ' );
+isa_ok( $in, 'Bio::SeqIO' );
-my $out = Bio::SeqIO->new(-format => 'pir',
- -fh => \*STDOUT);
+my $out = Bio::SeqIO->new(
+ -format => 'pir',
+ -fh => \*STDOUT
+);
-while (my $seq = $str->next_seq()) {
- ok( $seq->length > 1, 'checked length');
- $out->write_seq($seq) if $verbose > 0;
+while ( my $seq = $in->next_seq() ) {
+ ok( $seq->length > 1, 'checked length' );
+ $out->write_seq($seq) if $verbose > 0;
}
+
+# Empty description line
+$in = Bio::SeqIO->new(
+ -file => test_input_file('seqfile-no-desc.pir'),
+ -verbose => $verbose,
+ -format => 'pir'
+);
+my $seq = $in->next_seq();
+ok( $seq->seq =~ /^MGD/, 'Correct start' );
+$seq = $in->next_seq();
+ok( $seq->seq =~ /^GDV/, 'Correct start' );
+$seq = $in->next_seq();
+ok( $seq->seq =~ /^GDV/, 'Correct start' );
diff --git a/t/Tools/Phylo/PAML.t b/t/Tools/Phylo/PAML.t
deleted file mode 100644
index 21f7668..0000000
--- 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");
- at trees= $nssite_m0->get_trees;
-is (@trees , 1 );
-# model 0
-is($trees[0]->score, -30.819156);
-is($nssite_m1->model_num, "1");
- at 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;
-
- at 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');
- at 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/Tools/PrositeScan.t b/t/Tools/PrositeScan.t
new file mode 100644
index 0000000..bd983c5
--- /dev/null
+++ b/t/Tools/PrositeScan.t
@@ -0,0 +1,44 @@
+use strict;
+
+BEGIN {
+ use lib '.';
+ use Bio::Root::Test;
+
+ test_begin(-tests => 3);
+
+ use_ok('Bio::Tools::PrositeScan');
+ use_ok('Bio::SeqFeature::FeaturePair');
+}
+
+# Note: data generated by running
+#
+# ./ps_scan.pl --pfscan ./pfscan -d prosite.dat -o fasta \
+# t/data/test.fasta > t/data/ps_scan/out.PrositeScan
+#
+# followed by a manual removal of some of the output to simplify the test.
+
+subtest "Predictions" => sub {
+ my $factory = Bio::Tools::PrositeScan->new(
+ '-file' => test_input_file('ps_scan/out.PrositeScan'),
+ '-format' => 'fasta'
+ );
+
+ my $expected_matches = [
+ { seq_id => 'roa1_drome', coords => [253, 256], psac => 'PS00001', subseq => 'NNSF' },
+ { seq_id => 'roa1_drome', coords => [270, 273], psac => 'PS00001', subseq => 'NNSW' },
+ { seq_id => 'roa2_drome', coords => [344, 349], psac => 'PS00008', subseq => 'GNNQGF' },
+ { seq_id => 'roa2_drome', coords => [217, 355], psac => 'PS50321', subseq => re(qr/NR.{135}NN/) },
+ ];
+
+ my $actual_matches = [];
+ while( my $match = $factory->next_prediction ) {
+ push @$actual_matches, {
+ seq_id => $match->seq_id,
+ coords => [ $match->start, $match->end ],
+ psac => $match->hseq_id,
+ subseq => $match->feature1->seq->seq,
+ };
+ }
+
+ cmp_deeply( $actual_matches, $expected_matches, 'Comparing parsed prediction input' );
+};
diff --git a/t/data/M0.mlc b/t/data/M0.mlc
deleted file mode 100644
index 2594bf1..0000000
--- 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 b7125ff..0000000
--- 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 24da0ec..0000000
--- 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 d344524..0000000
--- 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 6046663..0000000
--- 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 db8b2ed..0000000
--- 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 6b4edfc..0000000
--- 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 8153199..0000000
--- 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 AC [...]
-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 ... ... ... ... ... ... ... .. [...]
-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. [...]
-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 .. [...]
-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.. .. [...]
-
-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 62a7593..0000000
--- 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 7cbdcdc..0000000
--- 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 [...]
-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 [...]
-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 [...]
-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 [...]
-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 [...]
-
-
-
-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 AC [...]
-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 ... ... ... ... ... ... ... .. [...]
-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. [...]
-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 .. [...]
-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.. .. [...]
-
- 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 81df32e..0000000
--- 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 C [...]
-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 C [...]
-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 C [...]
-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 C [...]
-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 C [...]
-
-
-
-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 GA [...]
-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. ... ... ... ... ... ... .. [...]
-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 ... ... ... ... ... .. [...]
-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 .. [...]
-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. ... .. [...]
-
- 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 58c228e..0000000
--- 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 a5dcdab..0000000
--- 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 AT [...]
-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 AT [...]
-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 AT [...]
-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 AT [...]
-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 AT [...]
-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 AT [...]
-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 [...]
-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 AT [...]
-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 AT [...]
-
-
-
-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 5ce2129..0000000
--- 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 aa903eb..0000000
--- 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 0e11124..0000000
--- 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 8ad8c27..0000000
--- 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 9deb9ed..0000000
--- 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 fd001c8..0000000
--- 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 1b61b0c..0000000
--- 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 0612464..0000000
--- 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 829927a..0000000
--- 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 [...]
-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 [...]
-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 [...]
-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 [...]
-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 [...]
-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 [...]
-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 [...]
-
-
-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 c09f49c..0000000
--- 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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AA [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-
-
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AA [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
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-
-
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AA [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-
-
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AA [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-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 AG [...]
-
-
diff --git a/t/data/codeml_lysozyme/rst1 b/t/data/codeml_lysozyme/rst1
deleted file mode 100644
index 205f0ed..0000000
--- 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 c9fb606..0000000
--- 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 63ded12..0000000
--- 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 bd15f69..0000000
--- 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 AA [...]
-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 AA [...]
-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 AA [...]
-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 AA [...]
-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 AA [...]
-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 AA [...]
-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 AA [...]
-
-
-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/ps_scan/out.PrositeScan b/t/data/ps_scan/out.PrositeScan
new file mode 100644
index 0000000..5740f08
--- /dev/null
+++ b/t/data/ps_scan/out.PrositeScan
@@ -0,0 +1,10 @@
+>roa1_drome/253-256 : PS00001 ASN_GLYCOSYLATION
+NNSF
+>roa1_drome/270-273 : PS00001 ASN_GLYCOSYLATION
+NNSW
+>roa2_drome/344-349 : PS00008 MYRISTYL
+GNNQGF
+>roa2_drome/217-355 : PS50321 ASN_RICH L=0
+NRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNN
+NPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAG
+GGNQGNYGNNQGFNNGGNN
diff --git a/t/data/seqfile-no-desc.pir b/t/data/seqfile-no-desc.pir
new file mode 100644
index 0000000..5b7da99
--- /dev/null
+++ b/t/data/seqfile-no-desc.pir
@@ -0,0 +1,9 @@
+>P1;CCHU
+
+MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+>P1;CCCZ
+
+GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+>P1;CCST
+
+GDVEK.GKKIF.VQKCAQCHTVEKGGKH.KTGPNLNGL.IGRKTGQAEGF.SYTEANKN.KGITWG.EETLM.EY.LENPKKY.IPGTKM.IF.AGIKKKAERADL.IAY.LKDATSK*
diff --git a/t/data/singleNSsite.mlc b/t/data/singleNSsite.mlc
deleted file mode 100644
index d39f622..0000000
--- 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/testaln.xmfa b/t/data/testaln.xmfa
index 420de46..dbe0f74 100644
--- a/t/data/testaln.xmfa
+++ b/t/data/testaln.xmfa
@@ -1,4 +1,4 @@
->1:1-598 + chrY
+>1:1-598 + chrY
TCCAAGTCGGCTTTATGTTTGCTTCTGCCAGGCATTCTAGATGCCCCATGTCTAGGATCT
CTTTAGGCAGGAGAGAGGGTGATGGTGTAGGAGGACCCATTTCTTGGCTTGCAGATTCCA
ATAATAAAAAAGTCACAGATTTAAACCCCAAACTTTGATGAAATGCAGGTCTAGGGTTTT
@@ -9,7 +9,7 @@ TTGAGCCCTTACCGTCCTGCCCCTAAACATCCAGACCTCAAGTTAGAGAGGGGAGTAACA
TTTGGGGGGTGCCCACACCTAGGAGGACCAATCCTTCTGGTTTCCTTAGGGATGCAGGAA
TTTGGGGGGGGGGGGCTCAGTGCTAAAACCAGTAGAGTCCTGGGCAAACGAGTATGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
->2:5000-5534 - chr17
+>2:5000-5534 - chr17
TGCAGATTGGCCTT-TGTTTCGTTTTTC-AAGCGTT-TAAA--CGCCTTGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGTGAACTGGGAAAACCTGGCTCTTCCTTTCGAGATTCCA
GTAACAAACATGTCATAACTATAAACGCCAAACTTGG--AGAGCGCAGGAATGGAAGGTC
@@ -20,7 +20,7 @@ TTCAGCTTTCCCCATCCAGCCA--ACGCAGGAAGGCCTGGAGCTACAGAGTTTAGAGCCA
TCTCTCCGCTGCTCAT--------TAACCAACCATTCCAGCT-------GTCTGTAGTGG
GTTTTTTTCTT----CTCTACACTAAAATGAGGACAGTCCAGGCCCTTTG--TTAGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
->3:19000-19537 - chr7
+>3:19000-19537 - chr7
TCCAGACTGTCTTT-TGCTCCCTTTTTCCGAGCATT-TAAAAATACCATGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGCGAGCTGGGAAGGCCTATTTCTTCATTTCGAGATTCTG
GTAATAAACATGTCATAAATATAAATGCCAAACTCCG--GAAATGCAGGTGTAGAGCGTC
@@ -32,10 +32,12 @@ TCTGTCCA-TGCTCTT--------TAACCAACCACTCCAGAT-------AGGTGTGGTGG
TTTTTTTTTTTTTTTCTCTGTACTAAAATTAGGACAGTCCAGGCCTGTTG--TTAGACCA
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
= score = 111
->1:1000-1059 + chrY
+>1:1000-1059 + chrY
CACTCTAATAGTAAAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCAT
->2:6000-6055 + chr17
+>2:6000-6055 + chr17
CACTCTAATACTAAACTTTCTTTTCCTCTCCACA----CTTTACTTTAATTACATCCCAT
->3:20000-20055 - chr12
+>3:20000-20055 - chr12
CACTCTAATAGTAAAGTTTCTT----TGTGCAGAAGCTCTTAGTTTTAATTAGATCCCAT
= score = 11
+>TelAviv_01:1-9 + TelAviv_01
+AAAAAAAAA
diff --git a/t/data/yn00.mlc b/t/data/yn00.mlc
deleted file mode 100644
index 03618af..0000000
--- 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 cf9182e..0000000
--- 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
-
diff --git a/travis_scripts/trigger-dockerhub.sh b/travis_scripts/trigger-dockerhub.sh
index 3674fa4..36bb789 100755
--- a/travis_scripts/trigger-dockerhub.sh
+++ b/travis_scripts/trigger-dockerhub.sh
@@ -25,6 +25,11 @@ if [[ -z "$DOCKERHUB_TOKEN" ]] ; then
exit 1
fi
+if [[ -n "$COVERAGE" && "$COVERAGE" != "0" ]] ; then
+ echo "Not triggering Docker Hub for code coverage build."
+ exit 0
+fi
+
## Should check for tag names that indicate release candidates rather
## than release names, and then skip those.
## However, this is already taken care of by the regular expression
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bioperl.git
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