5478 lines
340 KiB
Text
5478 lines
340 KiB
Text
perl-blead
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==========
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cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
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Work directory is /home/ryan/.cpanm/work/1493530045.29795
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You have make /usr/bin/make
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You have LWP 6.26
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You have /bin/tar: tar (GNU tar) 1.29
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Copyright (C) 2015 Free Software Foundation, Inc.
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License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
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This is free software: you are free to change and redistribute it.
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There is NO WARRANTY, to the extent permitted by law.
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Written by John Gilmore and Jay Fenlason.
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You have /usr/bin/unzip
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Searching Bio::BioStudio::Basic () on cpanmetadb ...
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Unpacking Bio-BioStudio-1.05.tar.gz
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--> Working on Bio::BioStudio::Basic
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Fetching http://www.cpan.org/authors/id/N/NO/NOTDOCTOR/Bio-BioStudio-1.05.tar.gz ... OK
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Bio-BioStudio-1.05
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Bio-BioStudio-1.05/Build.PL
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Bio-BioStudio-1.05/Changes
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Bio-BioStudio-1.05/ignore.txt
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Bio-BioStudio-1.05/Makefile.PL
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Bio-BioStudio-1.05/MANIFEST
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Bio-BioStudio-1.05/META.json
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Bio-BioStudio-1.05/META.yml
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Bio-BioStudio-1.05/README
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Bio-BioStudio-1.05/lib
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Bio-BioStudio-1.05/lib/Bio
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Bio-BioStudio-1.05/lib/Bio/BioStudio
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Basic.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/BLAST.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Cairo.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Chunk.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Diff.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Feature.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Foswiki.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/GBrowse.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/GFF3.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Git.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Marker.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Megachunk.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/MySQL.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/RestrictionEnzyme.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Diff
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Diff/Difference.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/Diff/Factory.pm
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Bio-BioStudio-1.05/lib/Bio/BioStudio/RestrictionEnzyme
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Bio-BioStudio-1.05/lib/Bio/BioStudio/RestrictionEnzyme/Store.pm
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Bio-BioStudio-1.05/t
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Bio-BioStudio-1.05/t/00-load.t
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Bio-BioStudio-1.05/t/boilerplate.t
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Bio-BioStudio-1.05/t/manifest.t
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Bio-BioStudio-1.05/t/pod-coverage.t
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Bio-BioStudio-1.05/t/pod.t
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Entering Bio-BioStudio-1.05
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Checking configure dependencies from META.json
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Checking if you have Module::Build 0.38 ... Yes (0.4222)
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Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
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Running Build.PL
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Configuring Bio-BioStudio-1.05 ... Checking prerequisites...
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requires:
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! Bio::GeneDesign::Basic is not installed
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! Bio::Tools::Run::StandAloneBlastPlus is not installed
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! Time::Format is not installed
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ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
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of the modules indicated above before proceeding with this installation
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Created MYMETA.yml and MYMETA.json
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Creating new 'Build' script for 'Bio-BioStudio' version '1.05'
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Checking dependencies from MYMETA.json ...
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Checking if you have Text::Wrap 2009.0305 ... Yes (2013.0523)
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Checking if you have Bio::Tools::Run::StandAloneBlastPlus 0 ... No
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Checking if you have Config::Auto 0.38 ... Yes (0.44)
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Checking if you have URI::Escape 1.59 ... Yes (3.31)
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Checking if you have Text::Diff 1.3 ... Yes (1.44)
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Checking if you have Cairo 1.09 ... Yes (1.106)
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Checking if you have Bio::Root::Root 0 ... Yes (undef)
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Checking if you have Time::Format 1.11 ... No
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Checking if you have DBI 1.616 ... Yes (1.636)
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Checking if you have Bio::GeneDesign::Basic 0 ... No
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Checking if you have Perl6::Slurp 0.03 ... Yes (0.051005)
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Checking if you have Test::More 0 ... Yes (1.302083)
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Checking if you have Digest::MD5 2.51 ... Yes (2.55)
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Searching Bio::Tools::Run::StandAloneBlastPlus (0) on cpanmetadb ...
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Unpacking BioPerl-Run-1.007001.tar.gz
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OK
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==> Found dependencies: Bio::Tools::Run::StandAloneBlastPlus, Time::Format, Bio::GeneDesign::Basic
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--> Working on Bio::Tools::Run::StandAloneBlastPlus
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Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.007001.tar.gz ... OK
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BioPerl-Run-1.007001
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BioPerl-Run-1.007001/.travis.yml
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BioPerl-Run-1.007001/AUTHORS
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BioPerl-Run-1.007001/Build.PL
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BioPerl-Run-1.007001/Changes
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BioPerl-Run-1.007001/DEPENDENCIES
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BioPerl-Run-1.007001/INSTALL
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BioPerl-Run-1.007001/INSTALL.PROGRAMS
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BioPerl-Run-1.007001/INSTALL.SKIP
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BioPerl-Run-1.007001/LICENSE
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BioPerl-Run-1.007001/MANIFEST
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BioPerl-Run-1.007001/META.json
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BioPerl-Run-1.007001/META.yml
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BioPerl-Run-1.007001/README.md
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BioPerl-Run-1.007001/lib
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BioPerl-Run-1.007001/lib/Bio
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BioPerl-Run-1.007001/lib/Bio/DB
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BioPerl-Run-1.007001/lib/Bio/DB/ESoap.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities.pm
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BioPerl-Run-1.007001/lib/Bio/DB/ESoap
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BioPerl-Run-1.007001/lib/Bio/DB/ESoap/WSDL.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/Result.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/FetchAdaptor
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm
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BioPerl-Run-1.007001/lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
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BioPerl-Run-1.007001/lib/Bio/Factory
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BioPerl-Run-1.007001/lib/Bio/Factory/EMBOSS.pm
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BioPerl-Run-1.007001/lib/Bio/Installer
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BioPerl-Run-1.007001/lib/Bio/Installer/Clustalw.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/EMBOSS.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/Generic.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/Hyphy.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/Muscle.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/PAML.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/Probcons.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/SLR.pm
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BioPerl-Run-1.007001/lib/Bio/Installer/TCoffee.pm
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BioPerl-Run-1.007001/lib/Bio/Tools
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BioPerl-Run-1.007001/lib/Bio/Tools/Run
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Analysis.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/AnalysisFactory.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/AssemblerBase.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BEDTools.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BlastPlus.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Bowtie.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BWA.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Cap3.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Coil.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/EMBOSSacd.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/EMBOSSApplication.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Ensembl.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Eponine.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/ERPIN.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/FootPrinter.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Genemark.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Genewise.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Genscan.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Glimmer.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Hmmer.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Infernal.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Maq.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Match.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/MCS.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Mdust.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Meme.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Minimo.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Newbler.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phrap.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Primate.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Primer3.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Prints.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Profile.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Promoterwise.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Pseudowise.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/RepeatMasker.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/RNAMotif.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Samtools.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Seg.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Signalp.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Simprot.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneBlast.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneWUBlast.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/TigrAssembler.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Tmhmm.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/TribeMCL.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/tRNAscanSE.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Vista.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/WrapperBase.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Amap.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Blat.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Clustalw.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/DBA.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Exonerate.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Gmap.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Kalign.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Lagan.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/MAFFT.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/MSAProbs.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Muscle.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Probalign.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Probcons.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Proda.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/Sim4.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Alignment/TCoffee.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Analysis
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Analysis/soap.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/AnalysisFactory
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/AnalysisFactory/soap.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BEDTools
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BEDTools/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BlastPlus
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BlastPlus/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Bowtie
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Bowtie/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BWA
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/BWA/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Maq
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Maq/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/FastTree.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Gerp.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Gumby.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/LVB.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PhyloBase.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phyml.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/QuickTree.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Raxml.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Semphy.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/SLR.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Molphy
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Njtree
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PAML
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phast
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Samtools
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/Samtools/Config.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneBlastPlus
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/WrapperBase
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BioPerl-Run-1.007001/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
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BioPerl-Run-1.007001/scripts
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BioPerl-Run-1.007001/scripts/bioperl_application_installer.PLS
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BioPerl-Run-1.007001/scripts/multi_hmmsearch.PLS
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BioPerl-Run-1.007001/scripts/panalysis.PLS
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BioPerl-Run-1.007001/scripts/papplmaker.PLS
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BioPerl-Run-1.007001/scripts/run_neighbor.PLS
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BioPerl-Run-1.007001/scripts/run_protdist.PLS
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BioPerl-Run-1.007001/t
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BioPerl-Run-1.007001/t/Amap.t
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BioPerl-Run-1.007001/t/Analysis_soap.t
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BioPerl-Run-1.007001/t/AnalysisFactory_soap.t
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BioPerl-Run-1.007001/t/BEDTools.t
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BioPerl-Run-1.007001/t/Blat.t
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BioPerl-Run-1.007001/t/Bowtie.t
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BioPerl-Run-1.007001/t/BWA.t
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BioPerl-Run-1.007001/t/Cap3.t
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BioPerl-Run-1.007001/t/Clustalw.t
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BioPerl-Run-1.007001/t/Coil.t
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BioPerl-Run-1.007001/t/Consense.t
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BioPerl-Run-1.007001/t/DBA.t
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BioPerl-Run-1.007001/t/DrawGram.t
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BioPerl-Run-1.007001/t/DrawTree.t
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BioPerl-Run-1.007001/t/EMBOSS.t
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BioPerl-Run-1.007001/t/Ensembl.t
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BioPerl-Run-1.007001/t/Eponine.t
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BioPerl-Run-1.007001/t/Exonerate.t
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BioPerl-Run-1.007001/t/FastTree.t
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BioPerl-Run-1.007001/t/FootPrinter.t
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BioPerl-Run-1.007001/t/Genemark.hmm.prokaryotic.t
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BioPerl-Run-1.007001/t/Genewise.t
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BioPerl-Run-1.007001/t/Genscan.t
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BioPerl-Run-1.007001/t/Gerp.t
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BioPerl-Run-1.007001/t/Glimmer2.t
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BioPerl-Run-1.007001/t/Glimmer3.t
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BioPerl-Run-1.007001/t/gmap-run.t
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BioPerl-Run-1.007001/t/Gumby.t
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BioPerl-Run-1.007001/t/Hmmer.t
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BioPerl-Run-1.007001/t/Hyphy.t
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BioPerl-Run-1.007001/t/Infernal.t
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BioPerl-Run-1.007001/t/Kalign.t
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BioPerl-Run-1.007001/t/Lagan.t
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BioPerl-Run-1.007001/t/LVB.t
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BioPerl-Run-1.007001/t/MAFFT.t
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BioPerl-Run-1.007001/t/Maq.t
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BioPerl-Run-1.007001/t/Match.t
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BioPerl-Run-1.007001/t/Mdust.t
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BioPerl-Run-1.007001/t/Meme.t
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BioPerl-Run-1.007001/t/Minimo.t
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BioPerl-Run-1.007001/t/Molphy.t
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BioPerl-Run-1.007001/t/MSAProbs.t
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BioPerl-Run-1.007001/t/Muscle.t
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BioPerl-Run-1.007001/t/Neighbor.t
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BioPerl-Run-1.007001/t/Newbler.t
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BioPerl-Run-1.007001/t/Njtree.t
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BioPerl-Run-1.007001/t/Pal2Nal.t
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BioPerl-Run-1.007001/t/PAML.t
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BioPerl-Run-1.007001/t/PhastCons.t
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BioPerl-Run-1.007001/t/Phrap.t
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BioPerl-Run-1.007001/t/Phyml.t
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BioPerl-Run-1.007001/t/Primate.t
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BioPerl-Run-1.007001/t/Primer3.t
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BioPerl-Run-1.007001/t/Prints.t
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BioPerl-Run-1.007001/t/Probalign.t
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BioPerl-Run-1.007001/t/Probcons.t
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BioPerl-Run-1.007001/t/Profile.t
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BioPerl-Run-1.007001/t/Promoterwise.t
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BioPerl-Run-1.007001/t/ProtDist.t
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BioPerl-Run-1.007001/t/ProtPars.t
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BioPerl-Run-1.007001/t/Pseudowise.t
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BioPerl-Run-1.007001/t/QuickTree.t
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BioPerl-Run-1.007001/t/Raxml.t
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BioPerl-Run-1.007001/t/RepeatMasker.t
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BioPerl-Run-1.007001/t/SABlastPlus.t
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BioPerl-Run-1.007001/t/Samtools.t
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BioPerl-Run-1.007001/t/Seg.t
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BioPerl-Run-1.007001/t/Semphy.t
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BioPerl-Run-1.007001/t/SeqBoot.t
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BioPerl-Run-1.007001/t/Signalp.t
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BioPerl-Run-1.007001/t/Sim4.t
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BioPerl-Run-1.007001/t/Simprot.t
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BioPerl-Run-1.007001/t/SLR.t
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BioPerl-Run-1.007001/t/SoapEU-function.t
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BioPerl-Run-1.007001/t/SoapEU-unit.t
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BioPerl-Run-1.007001/t/StandAloneFasta.t
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BioPerl-Run-1.007001/t/TCoffee.t
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BioPerl-Run-1.007001/t/TigrAssembler.t
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BioPerl-Run-1.007001/t/Tmhmm.t
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BioPerl-Run-1.007001/t/TribeMCL.t
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BioPerl-Run-1.007001/t/tRNAscanSE.t
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BioPerl-Run-1.007001/t/Vista.t
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BioPerl-Run-1.007001/t/data
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BioPerl-Run-1.007001/t/data/1.bg
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BioPerl-Run-1.007001/t/data/2.bg
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BioPerl-Run-1.007001/t/data/219877.cdna.fasta
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BioPerl-Run-1.007001/t/data/219877.tree
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BioPerl-Run-1.007001/t/data/277523.cdna.fasta
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BioPerl-Run-1.007001/t/data/277523.tree
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BioPerl-Run-1.007001/t/data/3.bg
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BioPerl-Run-1.007001/t/data/amino.fa
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BioPerl-Run-1.007001/t/data/apes.multi_fasta
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BioPerl-Run-1.007001/t/data/apes.newick
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BioPerl-Run-1.007001/t/data/blat_dna.fa
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BioPerl-Run-1.007001/t/data/campycoli.fas
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BioPerl-Run-1.007001/t/data/cel-cbr-fam.aln
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BioPerl-Run-1.007001/t/data/codeml.mlc
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BioPerl-Run-1.007001/t/data/coil_protein_input
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BioPerl-Run-1.007001/t/data/consense.treefile
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BioPerl-Run-1.007001/t/data/consensus.cns
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BioPerl-Run-1.007001/t/data/cysprot.fa
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BioPerl-Run-1.007001/t/data/cysprot.msf
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BioPerl-Run-1.007001/t/data/cysprot.raxml.tre
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BioPerl-Run-1.007001/t/data/cysprot.stockholm
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BioPerl-Run-1.007001/t/data/cysprot1a.fa
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BioPerl-Run-1.007001/t/data/cysprot1a.msf
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BioPerl-Run-1.007001/t/data/cysprot1b.fa
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BioPerl-Run-1.007001/t/data/cysprot1b.msf
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BioPerl-Run-1.007001/t/data/dba1a.fa
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BioPerl-Run-1.007001/t/data/dba1b.fa
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BioPerl-Run-1.007001/t/data/dba2.fa
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BioPerl-Run-1.007001/t/data/dna1.fa
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BioPerl-Run-1.007001/t/data/dna2.fa
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BioPerl-Run-1.007001/t/data/dna_seqs1.phy
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BioPerl-Run-1.007001/t/data/e_coli.bed3
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BioPerl-Run-1.007001/t/data/e_coli_1.bedpe
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BioPerl-Run-1.007001/t/data/e_coli_2.bedpe
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BioPerl-Run-1.007001/t/data/ecolitst.fa
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BioPerl-Run-1.007001/t/data/efetch_seq.wsdl
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BioPerl-Run-1.007001/t/data/elink_result.xml
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BioPerl-Run-1.007001/t/data/eponine.fa
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BioPerl-Run-1.007001/t/data/esearch_result.xml
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BioPerl-Run-1.007001/t/data/esum_result.xml
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BioPerl-Run-1.007001/t/data/eutils.wsdl
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BioPerl-Run-1.007001/t/data/exonerate_cdna.fa
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BioPerl-Run-1.007001/t/data/exonerate_cdna_rev.fa
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BioPerl-Run-1.007001/t/data/exonerate_genomic.fa
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BioPerl-Run-1.007001/t/data/exonerate_genomic_rev.fa
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BioPerl-Run-1.007001/t/data/fasta.fa
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BioPerl-Run-1.007001/t/data/fastalib.fa
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BioPerl-Run-1.007001/t/data/fastaprot.fa
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BioPerl-Run-1.007001/t/data/fontfile
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BioPerl-Run-1.007001/t/data/FootPrinter.seq.fa
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BioPerl-Run-1.007001/t/data/Ft.bam
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BioPerl-Run-1.007001/t/data/Ft.bed
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BioPerl-Run-1.007001/t/data/Ft.bed12
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BioPerl-Run-1.007001/t/data/Ft.frag.fas
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BioPerl-Run-1.007001/t/data/gb_result.xml
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BioPerl-Run-1.007001/t/data/Genscan.FastA
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BioPerl-Run-1.007001/t/data/gf-s85.phylip
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BioPerl-Run-1.007001/t/data/H_pylori_J99.fasta
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BioPerl-Run-1.007001/t/data/H_pylori_J99.glimmer2.icm
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BioPerl-Run-1.007001/t/data/H_pylori_J99.glimmer3.icm
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BioPerl-Run-1.007001/t/data/her2-edited.fasta
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BioPerl-Run-1.007001/t/data/hmmpfam_protein_input
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BioPerl-Run-1.007001/t/data/human.genomic
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BioPerl-Run-1.007001/t/data/hyphy1.fasta
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BioPerl-Run-1.007001/t/data/hyphy1.tree
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BioPerl-Run-1.007001/t/data/lagan_dna.fa
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BioPerl-Run-1.007001/t/data/longnames.aln
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BioPerl-Run-1.007001/t/data/lvb.fa
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BioPerl-Run-1.007001/t/data/lvb_sequential.phy
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BioPerl-Run-1.007001/t/data/neighbor.dist
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BioPerl-Run-1.007001/t/data/new_dna.fa
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BioPerl-Run-1.007001/t/data/new_pep.fa
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BioPerl-Run-1.007001/t/data/njtree_aln2.nucl.mfa
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BioPerl-Run-1.007001/t/data/NM_002254.gb
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BioPerl-Run-1.007001/t/data/NM_002254.tfa
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BioPerl-Run-1.007001/t/data/pal2nal.aln
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BioPerl-Run-1.007001/t/data/pal2nal.nuc
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BioPerl-Run-1.007001/t/data/pfam_sample_R11
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BioPerl-Run-1.007001/t/data/Phrap.fa
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BioPerl-Run-1.007001/t/data/primate_query.fa
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BioPerl-Run-1.007001/t/data/primate_target.fa
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BioPerl-Run-1.007001/t/data/Primer3.fa
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BioPerl-Run-1.007001/t/data/prints.dat
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BioPerl-Run-1.007001/t/data/Prints_prot.FastA
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BioPerl-Run-1.007001/t/data/profile_prot.FastA
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BioPerl-Run-1.007001/t/data/prosite.dat
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BioPerl-Run-1.007001/t/data/protpars.phy
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BioPerl-Run-1.007001/t/data/ps1.fa
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BioPerl-Run-1.007001/t/data/purine.1.sto
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BioPerl-Run-1.007001/t/data/purine.added.fa
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BioPerl-Run-1.007001/t/data/purine.all.fa
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BioPerl-Run-1.007001/t/data/purine.c.cm
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BioPerl-Run-1.007001/t/data/purine.cm
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BioPerl-Run-1.007001/t/data/r1.fq
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BioPerl-Run-1.007001/t/data/r1bwa.fq
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BioPerl-Run-1.007001/t/data/r2.fq
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BioPerl-Run-1.007001/t/data/r2bwa.fq
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BioPerl-Run-1.007001/t/data/repeatmasker.fa
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BioPerl-Run-1.007001/t/data/road.pep
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BioPerl-Run-1.007001/t/data/sample_dataset_1.fa
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BioPerl-Run-1.007001/t/data/sample_dataset_1.qual
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BioPerl-Run-1.007001/t/data/sample_dataset_1_aligned.fa
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BioPerl-Run-1.007001/t/data/segmask_data.asn
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BioPerl-Run-1.007001/t/data/semphy.seq
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BioPerl-Run-1.007001/t/data/semphy.tree
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BioPerl-Run-1.007001/t/data/signalp_input_protein
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BioPerl-Run-1.007001/t/data/sim4_cdna.fa
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BioPerl-Run-1.007001/t/data/sim4_database.fa
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BioPerl-Run-1.007001/t/data/sim4_genomic.fa
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BioPerl-Run-1.007001/t/data/simprot_tree.nh
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BioPerl-Run-1.007001/t/data/species_tree_njtree.nh
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BioPerl-Run-1.007001/t/data/test-aln.msf
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BioPerl-Run-1.007001/t/data/test-query.fas
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BioPerl-Run-1.007001/t/data/test-spa-p.fas
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BioPerl-Run-1.007001/t/data/test-spa.fas
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BioPerl-Run-1.007001/t/data/test.txt
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BioPerl-Run-1.007001/t/data/test_prot.FastA
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BioPerl-Run-1.007001/t/data/testaln.phylip
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BioPerl-Run-1.007001/t/data/transfac.dat
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BioPerl-Run-1.007001/t/data/tree_of_life
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BioPerl-Run-1.007001/t/data/treefile.example
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BioPerl-Run-1.007001/t/data/TribeMCL.bls
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BioPerl-Run-1.007001/t/data/TribeMCL.desc
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BioPerl-Run-1.007001/t/data/vista.cls
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BioPerl-Run-1.007001/t/data/vista.gff
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BioPerl-Run-1.007001/t/data/xprt.gb
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BioPerl-Run-1.007001/t/data/bowtie
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BioPerl-Run-1.007001/t/data/bowtie/indexes
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.1.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.2.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.3.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.4.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.rev.1.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.rev.2.ebwt
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BioPerl-Run-1.007001/t/data/bowtie/reads
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli.cb
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.fa
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.fq
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.raw
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_10000snp.fa
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_10000snp.fq
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_1.fa
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_1.fq
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_2.fa
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BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_2.fq
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BioPerl-Run-1.007001/t/data/gerp
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BioPerl-Run-1.007001/t/data/gerp/ENr111.gerp.tree
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BioPerl-Run-1.007001/t/data/gerp/ENr111.mfa.gz
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BioPerl-Run-1.007001/t/data/gumby
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BioPerl-Run-1.007001/t/data/gumby/hmrd.mfa
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BioPerl-Run-1.007001/t/data/gumby/hmrd.tree
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BioPerl-Run-1.007001/t/data/gumby/human.gff
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BioPerl-Run-1.007001/t/data/gumby/readme.txt
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BioPerl-Run-1.007001/t/data/taxdump
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BioPerl-Run-1.007001/t/data/taxdump/names.dmp
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BioPerl-Run-1.007001/t/data/taxdump/nodes.dmp
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BioPerl-Run-1.007001/t/Tools
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BioPerl-Run-1.007001/t/Tools/Run
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BioPerl-Run-1.007001/t/Tools/Run/Dummy.pm
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BioPerl-Run-1.007001/t/Tools/Run/RemoteBlast.t
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BioPerl-Run-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
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BioPerl-Run-1.007001/t/Tools/Run/StandAloneBlast.t
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BioPerl-Run-1.007001/t/Tools/Run/WBCommandExts.t
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BioPerl-Run-1.007001/t/Tools/Run/WrapperBase.t
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BioPerl-Run-1.007001/t/Tools/Run/Dummy
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BioPerl-Run-1.007001/t/Tools/Run/Dummy/Config.pm
|
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Entering BioPerl-Run-1.007001
|
|
Checking configure dependencies from META.json
|
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Checking if you have Module::Build 0.42 ... Yes (0.4222)
|
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Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
|
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Running Build.PL
|
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Configuring BioPerl-Run-1.007001 ... Install scripts? y/n [n ]n
|
|
Do you want to run tests that require connection to servers across the internet
|
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(likely to cause some failures)? y/n [n ]n
|
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- will not run internet-requiring tests
|
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Created MYMETA.yml and MYMETA.json
|
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Creating new 'Build' script for 'BioPerl-Run' version '1.007001'
|
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Checking dependencies from MYMETA.json ...
|
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Checking if you have Bio::Root::Version 1.007000 ... Yes (1.007001)
|
|
Checking if you have Bio::Root::Root 0 ... Yes (undef)
|
|
Checking if you have Bio::Root::Test 0 ... Yes (undef)
|
|
OK
|
|
Building and testing BioPerl-Run-1.007001 ... Building BioPerl-Run
|
|
# Required executable for Bio::Tools::Run::Alignment::Amap is not present
|
|
t/Amap.t ...................... ok
|
|
t/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested
|
|
t/Analysis_soap.t ............. skipped: Network tests have not been requested
|
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# Required executable for Bio::Tools::Run::BEDTools is not present
|
|
t/BEDTools.t .................. ok
|
|
# Required executable for Bio::Tools::Run::BWA is not present
|
|
t/BWA.t ....................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
|
|
t/Blat.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Bowtie is not present
|
|
t/Bowtie.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Cap3 is not present
|
|
t/Cap3.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Clustalw is not present
|
|
t/Clustalw.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Coil is not present
|
|
t/Coil.t ...................... ok
|
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# Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present
|
|
t/Consense.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Alignment::DBA is not present
|
|
t/DBA.t ....................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
|
|
t/DrawGram.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
|
|
t/DrawTree.t .................. ok
|
|
t/EMBOSS.t .................... ok
|
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t/Ensembl.t ................... skipped: Network tests have not been requested
|
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# Looks like you planned 7 tests but ran 2.
|
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t/Eponine.t ...................
|
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Dubious, test returned 255 (wstat 65280, 0xff00)
|
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Failed 5/7 subtests
|
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# Required executable for Bio::Tools::Run::Alignment::Exonerate is not present
|
|
t/Exonerate.t ................. ok
|
|
# Required executable for Bio::Tools::Run::Phylo::FastTree is not present
|
|
t/FastTree.t .................. ok
|
|
# Required executable for Bio::Tools::Run::FootPrinter is not present
|
|
t/FootPrinter.t ............... ok
|
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# Required environment variable $GENEMARK_MODELS is not set
|
|
t/Genemark.hmm.prokaryotic.t .. ok
|
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# Required executable for Bio::Tools::Run::Genewise is not present
|
|
t/Genewise.t .................. ok
|
|
# Required environment variable $GENSCANDIR is not set
|
|
t/Genscan.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Gerp is not present
|
|
t/Gerp.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Glimmer is not present
|
|
t/Glimmer2.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Glimmer is not present
|
|
t/Glimmer3.t .................. ok
|
|
|
|
# Failed test 'use Bio::Tools::Run::Phylo::Gumby;'
|
|
# at t/Gumby.t line 10.
|
|
# Tried to use 'Bio::Tools::Run::Phylo::Gumby'.
|
|
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Tools/Phylo/Gumby.pm line 83.
|
|
# BEGIN failed--compilation aborted at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Tools/Phylo/Gumby.pm line 83.
|
|
# Compilation failed in require at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
|
|
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
|
|
# Compilation failed in require at t/Gumby.t line 10.
|
|
# BEGIN failed--compilation aborted at t/Gumby.t line 10.
|
|
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Gumby" at t/Gumby.t line 25.
|
|
# Looks like your test exited with 255 just after 8.
|
|
t/Gumby.t .....................
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 117/124 subtests
|
|
# Required executable for Bio::Tools::Run::Hmmer is not present
|
|
t/Hmmer.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Hyphy::REL is not present
|
|
t/Hyphy.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Infernal is not present
|
|
t/Infernal.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Kalign is not present
|
|
t/Kalign.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
|
|
t/LVB.t ....................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
|
|
t/Lagan.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::MAFFT is not present
|
|
t/MAFFT.t ..................... ok
|
|
|
|
# Failed test 'use Bio::Tools::Run::MCS;'
|
|
# at t/MCS.t line 9.
|
|
# Tried to use 'Bio::Tools::Run::MCS'.
|
|
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/MCS.pm line 131.
|
|
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/MCS.pm line 131.
|
|
# Compilation failed in require at t/MCS.t line 9.
|
|
# BEGIN failed--compilation aborted at t/MCS.t line 9.
|
|
|
|
# Failed test 'use Bio::SeqFeature::Annotated;'
|
|
# at t/MCS.t line 10.
|
|
# Tried to use 'Bio::SeqFeature::Annotated'.
|
|
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at t/MCS.t line 10.
|
|
# BEGIN failed--compilation aborted at t/MCS.t line 10.
|
|
Can't locate object method "new" via package "Bio::Tools::Run::MCS" at t/MCS.t line 18.
|
|
# Looks like your test exited with 255 just after 4.
|
|
t/MCS.t .......................
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 22/24 subtests
|
|
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
|
|
t/MSAProbs.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Maq is not present
|
|
t/Maq.t ....................... ok
|
|
|
|
# Failed test 'use Bio::Tools::Run::Match;'
|
|
# at t/Match.t line 10.
|
|
# Tried to use 'Bio::Tools::Run::Match'.
|
|
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Match.pm line 116.
|
|
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Match.pm line 116.
|
|
# Compilation failed in require at t/Match.t line 10.
|
|
# BEGIN failed--compilation aborted at t/Match.t line 10.
|
|
Can't locate object method "new" via package "Bio::Tools::Run::Match" at t/Match.t line 17.
|
|
# Looks like your test exited with 255 just after 1.
|
|
t/Match.t .....................
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 7/7 subtests
|
|
# Required executable for Bio::Tools::Run::Mdust is not present
|
|
t/Mdust.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Meme is not present
|
|
t/Meme.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Minimo is not present
|
|
t/Minimo.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
|
|
t/Molphy.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Muscle is not present
|
|
t/Muscle.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
|
|
t/Neighbor.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Newbler is not present
|
|
t/Newbler.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
|
|
t/Njtree.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present
|
|
t/PAML.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
|
|
t/Pal2Nal.t ................... ok
|
|
|
|
# Failed test 'use Bio::Tools::Run::Phylo::Phast::PhastCons;'
|
|
# at t/PhastCons.t line 10.
|
|
# Tried to use 'Bio::Tools::Run::Phylo::Phast::PhastCons'.
|
|
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
|
|
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493530045.29795/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
|
|
# Compilation failed in require at t/PhastCons.t line 10.
|
|
# BEGIN failed--compilation aborted at t/PhastCons.t line 10.
|
|
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Phast::PhastCons" at t/PhastCons.t line 23.
|
|
# Looks like your test exited with 255 just after 6.
|
|
t/PhastCons.t .................
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 176/181 subtests
|
|
# Required executable for Bio::Tools::Run::Phrap is not present
|
|
t/Phrap.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phyml is not present
|
|
t/Phyml.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Primate is not present
|
|
t/Primate.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Primer3 is not present
|
|
t/Primer3.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Prints is not present
|
|
t/Prints.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
|
|
t/Probalign.t ................. ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Probcons is not present
|
|
t/Probcons.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Profile is not present
|
|
t/Profile.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Promoterwise is not present
|
|
t/Promoterwise.t .............. ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
|
|
t/ProtDist.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
|
|
t/ProtPars.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Pseudowise is not present
|
|
t/Pseudowise.t ................ ok
|
|
# Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
|
|
t/QuickTree.t ................. ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Raxml is not present
|
|
t/Raxml.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::RepeatMasker is not present
|
|
t/RepeatMasker.t .............. ok
|
|
# Required executable for Bio::Tools::Run::BlastPlus is not present
|
|
# Looks like you planned 73 tests but ran 69.
|
|
t/SABlastPlus.t ...............
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 4/73 subtests
|
|
(less 65 skipped subtests: 4 okay)
|
|
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
|
|
t/SLR.t ....................... ok
|
|
# Required executable for Bio::Tools::Run::Samtools is not present
|
|
t/Samtools.t .................. ok
|
|
# Required executable for Bio::Tools::Run::Seg is not present
|
|
t/Seg.t ....................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
|
|
t/Semphy.t .................... ok
|
|
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
|
|
t/SeqBoot.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Signalp is not present
|
|
t/Signalp.t ................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Sim4 is not present
|
|
t/Sim4.t ...................... ok
|
|
# Required executable for Bio::Tools::Run::Simprot is not present
|
|
t/Simprot.t ................... ok
|
|
t/SoapEU-function.t ........... skipped: Valid email not provided; required for tests
|
|
# NCBI SOAP EUtilities API no longer supported as of 2015, modules are deprecated and will be removed in a future release
|
|
t/SoapEU-unit.t ............... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
|
|
t/StandAloneFasta.t ........... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::TCoffee is not present
|
|
t/TCoffee.t ................... ok
|
|
# Required executable for Bio::Tools::Run::TigrAssembler is not present
|
|
# Required executable for Bio::Tools::Run::TigrAssembler is not present
|
|
t/TigrAssembler.t ............. ok
|
|
# Required executable for Bio::Tools::Run::Tmhmm is not present
|
|
t/Tmhmm.t ..................... ok
|
|
t/TribeMCL.t .................. ok
|
|
t/Vista.t ..................... ok
|
|
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
|
|
t/gmap-run.t .................. ok
|
|
# Required executable for Bio::Tools::Run::tRNAscanSE is not present
|
|
t/tRNAscanSE.t ................ ok
|
|
|
|
Test Summary Report
|
|
-------------------
|
|
t/Eponine.t (Wstat: 65280 Tests: 2 Failed: 0)
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 7 tests but ran 2.
|
|
t/Gumby.t (Wstat: 65280 Tests: 8 Failed: 1)
|
|
Failed test: 1
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 124 tests but ran 8.
|
|
t/MCS.t (Wstat: 65280 Tests: 4 Failed: 2)
|
|
Failed tests: 1-2
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 24 tests but ran 4.
|
|
t/Match.t (Wstat: 65280 Tests: 1 Failed: 1)
|
|
Failed test: 1
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 7 tests but ran 1.
|
|
t/PhastCons.t (Wstat: 65280 Tests: 6 Failed: 1)
|
|
Failed test: 1
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 181 tests but ran 6.
|
|
t/SABlastPlus.t (Wstat: 65280 Tests: 69 Failed: 0)
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 73 tests but ran 69.
|
|
Files=83, Tests=2767, 8 wallclock secs ( 0.21 usr 0.06 sys + 6.96 cusr 0.55 csys = 7.78 CPU)
|
|
Result: FAIL
|
|
Failed 6/83 test programs. 5/2767 subtests failed.
|
|
! Installing Bio::Tools::Run::StandAloneBlastPlus failed. See /home/ryan/.cpanm/work/1493530045.29795/build.log for details. Retry with --force to force install it.
|
|
Searching Time::Format (1.11) on cpanmetadb ...
|
|
Unpacking Time-Format-1.12.tar.gz
|
|
FAIL
|
|
--> Working on Time::Format
|
|
Fetching http://www.cpan.org/authors/id/R/RO/ROODE/Time-Format-1.12.tar.gz ... OK
|
|
Time-Format-1.12
|
|
Time-Format-1.12/Build.PL
|
|
Time-Format-1.12/Changes
|
|
Time-Format-1.12/Makefile.PL
|
|
Time-Format-1.12/MANIFEST
|
|
Time-Format-1.12/MANIFEST.SKIP
|
|
Time-Format-1.12/META.json
|
|
Time-Format-1.12/META.yml
|
|
Time-Format-1.12/quickref.ps
|
|
Time-Format-1.12/quickref.txt
|
|
Time-Format-1.12/README
|
|
Time-Format-1.12/SIGNATURE
|
|
Time-Format-1.12/lib
|
|
Time-Format-1.12/lib/Time
|
|
Time-Format-1.12/lib/Time/Format.pm
|
|
Time-Format-1.12/t
|
|
Time-Format-1.12/t/0-signature.t
|
|
Time-Format-1.12/t/1-load.t
|
|
Time-Format-1.12/t/DateManip.t
|
|
Time-Format-1.12/t/DateTime.t
|
|
Time-Format-1.12/t/die.t
|
|
Time-Format-1.12/t/doc.t
|
|
Time-Format-1.12/t/epoch.t
|
|
Time-Format-1.12/t/export1.t
|
|
Time-Format-1.12/t/export2.t
|
|
Time-Format-1.12/t/export3.t
|
|
Time-Format-1.12/t/funcs.t
|
|
Time-Format-1.12/t/locale.t
|
|
Time-Format-1.12/t/manip.t
|
|
Time-Format-1.12/t/msec.t
|
|
Time-Format-1.12/t/past.t
|
|
Time-Format-1.12/t/quot.t
|
|
Time-Format-1.12/t/strftime.t
|
|
Time-Format-1.12/t/string.t
|
|
Time-Format-1.12/t/time.t
|
|
Time-Format-1.12/t/xs_DateTime.t
|
|
Time-Format-1.12/t/xs_doc.t
|
|
Time-Format-1.12/t/xs_funcs.t
|
|
Time-Format-1.12/t/xs_locale.t
|
|
Time-Format-1.12/t/xs_quot.t
|
|
Time-Format-1.12/t/xs_time.t
|
|
Entering Time-Format-1.12
|
|
Checking configure dependencies from META.json
|
|
Checking if you have Module::Build 0.4 ... Yes (0.4222)
|
|
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
|
|
Running Build.PL
|
|
Configuring Time-Format-1.12 ... Created MYMETA.yml and MYMETA.json
|
|
Creating new 'Build' script for 'Time-Format' version '1.12'
|
|
Checking dependencies from MYMETA.json ...
|
|
Checking if you have Test::Simple 0.40 ... Yes (1.302083)
|
|
Checking if you have Time::Local 1.07 ... Yes (1.25)
|
|
OK
|
|
Building and testing Time-Format-1.12 ... Building Time-Format
|
|
t/0-signature.t .. ok
|
|
t/1-load.t ....... ok
|
|
t/DateManip.t .... ok
|
|
t/DateTime.t ..... ok
|
|
t/die.t .......... ok
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/TZ.pm line 1518, <DATA> line 1.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/TZ.pm line 1518, <DATA> line 1.
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/TZ.pm line 1518, <DATA> line 1.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/TZ.pm line 1518, <DATA> line 1.
|
|
Can't locate object method "_now" via package "Date::Manip::TZ" at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/TZ.pm line 1518, <DATA> line 1.
|
|
# Looks like your test exited with 255 just after 23.
|
|
t/doc.t ..........
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 3/26 subtests
|
|
t/epoch.t ........ ok
|
|
t/export1.t ...... ok
|
|
t/export2.t ...... ok
|
|
t/export3.t ...... ok
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146, <DATA> line 1.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146, <DATA> line 1.
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146, <DATA> line 1.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146, <DATA> line 1.
|
|
Can't locate object method "_fix_year" via package "Date::Manip::TZ" at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146, <DATA> line 1.
|
|
# Looks like your test exited with 255 just after 12.
|
|
t/funcs.t ........
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 6/18 subtests
|
|
t/locale.t ....... ok
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146.
|
|
Can't locate package Date::Manip::Obj for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146.
|
|
Can't locate package Date::Manip::TZ_Base for @Date::Manip::TZ::ISA at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146.
|
|
Can't locate object method "_fix_year" via package "Date::Manip::TZ" at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Date/Manip/Date.pm line 2146.
|
|
# Looks like your test exited with 255 just after 1.
|
|
t/manip.t ........
|
|
Dubious, test returned 255 (wstat 65280, 0xff00)
|
|
Failed 5/6 subtests
|
|
t/msec.t ......... ok
|
|
t/past.t ......... ok
|
|
t/quot.t ......... ok
|
|
t/strftime.t ..... ok
|
|
t/string.t ....... ok
|
|
t/time.t ......... ok
|
|
t/xs_DateTime.t .. ok
|
|
t/xs_doc.t ....... ok
|
|
t/xs_funcs.t ..... ok
|
|
t/xs_locale.t .... ok
|
|
t/xs_quot.t ...... ok
|
|
t/xs_time.t ...... ok
|
|
|
|
Test Summary Report
|
|
-------------------
|
|
t/doc.t (Wstat: 65280 Tests: 23 Failed: 0)
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 26 tests but ran 23.
|
|
t/funcs.t (Wstat: 65280 Tests: 12 Failed: 0)
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 18 tests but ran 12.
|
|
t/manip.t (Wstat: 65280 Tests: 1 Failed: 0)
|
|
Non-zero exit status: 255
|
|
Parse errors: Bad plan. You planned 6 tests but ran 1.
|
|
Files=25, Tests=459, 5 wallclock secs ( 0.06 usr 0.02 sys + 1.06 cusr 0.10 csys = 1.24 CPU)
|
|
Result: FAIL
|
|
Failed 3/25 test programs. 0/459 subtests failed.
|
|
! Installing Time::Format failed. See /home/ryan/.cpanm/work/1493530045.29795/build.log for details. Retry with --force to force install it.
|
|
Searching Bio::GeneDesign::Basic (0) on cpanmetadb ...
|
|
Unpacking Bio-GeneDesign-5.54.tar.gz
|
|
FAIL
|
|
--> Working on Bio::GeneDesign::Basic
|
|
Fetching http://www.cpan.org/authors/id/N/NO/NOTDOCTOR/Bio-GeneDesign-5.54.tar.gz ... OK
|
|
Bio-GeneDesign-5.54
|
|
Bio-GeneDesign-5.54/Build.PL
|
|
Bio-GeneDesign-5.54/Changes
|
|
Bio-GeneDesign-5.54/Makefile.PL
|
|
Bio-GeneDesign-5.54/MANIFEST
|
|
Bio-GeneDesign-5.54/META.json
|
|
Bio-GeneDesign-5.54/META.yml
|
|
Bio-GeneDesign-5.54/README
|
|
Bio-GeneDesign-5.54/ToDo
|
|
Bio-GeneDesign-5.54/bin
|
|
Bio-GeneDesign-5.54/bin/GD_Filter_Enzymes.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Generate_RSCU_Table.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Graph_Dotplot.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Graph_RSCU_Values.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Juggle_Codons.pl
|
|
Bio-GeneDesign-5.54/bin/GD_List_Codon_Tables.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Repeat_Smash.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Reverse_Translate.pl
|
|
Bio-GeneDesign-5.54/bin/GD_Sequence_Subtraction.pl
|
|
Bio-GeneDesign-5.54/codon_tables
|
|
Bio-GeneDesign-5.54/codon_tables/Arabidopsis_thaliana.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Bacillus_subtilis.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Caenorhabditis_elegans.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Corynebacterium_glutamicum.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Deinococcus_radiodurans.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Drosophila_melanogaster.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Escherichia_coli.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Homo_sapiens.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Mycoplasma_genitalium.ct
|
|
Bio-GeneDesign-5.54/codon_tables/Mycoplasma_genitalium.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Oryza_sativa.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Saccharomyces_cerevisiae.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Standard.ct
|
|
Bio-GeneDesign-5.54/codon_tables/Unbiased.rscu
|
|
Bio-GeneDesign-5.54/codon_tables/Yarrowia_lipolytica.rscu
|
|
Bio-GeneDesign-5.54/enzymes
|
|
Bio-GeneDesign-5.54/enzymes/all_enzymes
|
|
Bio-GeneDesign-5.54/enzymes/blunts
|
|
Bio-GeneDesign-5.54/enzymes/IIB
|
|
Bio-GeneDesign-5.54/enzymes/nonpal
|
|
Bio-GeneDesign-5.54/enzymes/nonpal_and_IIB
|
|
Bio-GeneDesign-5.54/enzymes/nonpal_short
|
|
Bio-GeneDesign-5.54/enzymes/outside
|
|
Bio-GeneDesign-5.54/enzymes/standard
|
|
Bio-GeneDesign-5.54/enzymes/standard_and_IIB
|
|
Bio-GeneDesign-5.54/enzymes/test
|
|
Bio-GeneDesign-5.54/lib
|
|
Bio-GeneDesign-5.54/lib/Bio
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Basic.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/CodonJuggle.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Codons.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Graph.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Oligo.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/PrefixTree.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/Random.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/RestrictionEnzyme.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/RestrictionEnzymes.pm
|
|
Bio-GeneDesign-5.54/lib/Bio/GeneDesign/ReverseTranslate.pm
|
|
Bio-GeneDesign-5.54/t
|
|
Bio-GeneDesign-5.54/t/00-load.t
|
|
Bio-GeneDesign-5.54/t/10-basic.t
|
|
Bio-GeneDesign-5.54/t/12-io.t
|
|
Bio-GeneDesign-5.54/t/15-codons.t
|
|
Bio-GeneDesign-5.54/t/20-reverse_translate.t
|
|
Bio-GeneDesign-5.54/t/25-codon_juggle.t
|
|
Bio-GeneDesign-5.54/t/30-enzymes.t
|
|
Bio-GeneDesign-5.54/t/35-subtract_sequence.t
|
|
Bio-GeneDesign-5.54/t/40-graph.t
|
|
Bio-GeneDesign-5.54/t/60-prefix.t
|
|
Bio-GeneDesign-5.54/t/65-random.t
|
|
Bio-GeneDesign-5.54/t/boilerplate.t
|
|
Bio-GeneDesign-5.54/t/manifest.t
|
|
Bio-GeneDesign-5.54/t/pod-coverage.t
|
|
Bio-GeneDesign-5.54/t/pod.t
|
|
Bio-GeneDesign-5.54/t/testagene.fasta
|
|
Bio-GeneDesign-5.54/t/testr_GRV_yeast.gif
|
|
Entering Bio-GeneDesign-5.54
|
|
Checking configure dependencies from META.json
|
|
Checking if you have Module::Build 0.38 ... Yes (0.4222)
|
|
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
|
|
Running Build.PL
|
|
Configuring Bio-GeneDesign-5.54 ...
|
|
Checking prerequisites...
|
|
requires:
|
|
! Bio::Root::Root (0) is installed, but we need version >= 1.006924
|
|
|
|
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
|
|
of the modules indicated above before proceeding with this installation
|
|
|
|
Where should configuration files be installed? [/etc/GeneDesign/ ]/etc/GeneDesign/
|
|
Where should scripts be installed? [/usr/local/bin/ ]/usr/local/bin/
|
|
Where should GeneDesign write tmp files? [/tmp/ ]/tmp/
|
|
Enable GD::Graphics support? [Y ]Y
|
|
Configuration files will be in /etc/GeneDesign/
|
|
Scripts will be in /usr/local/bin/
|
|
Temporary files will be written to /tmp/
|
|
Installing graphics support
|
|
|
|
Created MYMETA.yml and MYMETA.json
|
|
Creating new 'Build' script for 'Bio-GeneDesign' version '5.54'
|
|
|
|
Checking dependencies from MYMETA.json ...
|
|
Checking if you have Test::More 0.8 ... Yes (1.302083)
|
|
Checking if you have Text::Wrap 2009.0305 ... Yes (2013.0523)
|
|
Checking if you have Bio::Root::Root 1.006924 ... No
|
|
Checking if you have List::Util 1.22 ... Yes (1.47)
|
|
Checking if you have Math::Combinatorics 0.09 ... Yes (0.09)
|
|
Checking if you have Test::Deep 0.1 ... Yes (1.126)
|
|
Searching Bio::Root::Root (1.006924) on cpanmetadb ...
|
|
Unpacking BioPerl-1.007001.tar.gz
|
|
OK
|
|
==> Found dependencies: Bio::Root::Root
|
|
--> Working on Bio::Root::Root
|
|
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ... OK
|
|
BioPerl-1.007001
|
|
BioPerl-1.007001/.travis.yml
|
|
BioPerl-1.007001/AUTHORS
|
|
BioPerl-1.007001/BioPerl.pm
|
|
BioPerl-1.007001/BUGS
|
|
BioPerl-1.007001/Build.PL
|
|
BioPerl-1.007001/Changes
|
|
BioPerl-1.007001/DEPENDENCIES
|
|
BioPerl-1.007001/DEPRECATED
|
|
BioPerl-1.007001/INSTALL-WIN.md
|
|
BioPerl-1.007001/INSTALL.md
|
|
BioPerl-1.007001/INSTALL.SKIP
|
|
BioPerl-1.007001/LICENSE
|
|
BioPerl-1.007001/MANIFEST
|
|
BioPerl-1.007001/META.json
|
|
BioPerl-1.007001/META.yml
|
|
BioPerl-1.007001/README.md
|
|
BioPerl-1.007001/Bio
|
|
BioPerl-1.007001/Bio/AlignIO.pm
|
|
BioPerl-1.007001/Bio/AnalysisI.pm
|
|
BioPerl-1.007001/Bio/AnalysisParserI.pm
|
|
BioPerl-1.007001/Bio/AnalysisResultI.pm
|
|
BioPerl-1.007001/Bio/AnnotatableI.pm
|
|
BioPerl-1.007001/Bio/AnnotationCollectionI.pm
|
|
BioPerl-1.007001/Bio/AnnotationI.pm
|
|
BioPerl-1.007001/Bio/ClusterI.pm
|
|
BioPerl-1.007001/Bio/ClusterIO.pm
|
|
BioPerl-1.007001/Bio/DasI.pm
|
|
BioPerl-1.007001/Bio/DBLinkContainerI.pm
|
|
BioPerl-1.007001/Bio/DescribableI.pm
|
|
BioPerl-1.007001/Bio/FeatureHolderI.pm
|
|
BioPerl-1.007001/Bio/HandlerBaseI.pm
|
|
BioPerl-1.007001/Bio/IdCollectionI.pm
|
|
BioPerl-1.007001/Bio/IdentifiableI.pm
|
|
BioPerl-1.007001/Bio/LocatableSeq.pm
|
|
BioPerl-1.007001/Bio/LocationI.pm
|
|
BioPerl-1.007001/Bio/MapIO.pm
|
|
BioPerl-1.007001/Bio/NexmlIO.pm
|
|
BioPerl-1.007001/Bio/OntologyIO.pm
|
|
BioPerl-1.007001/Bio/ParameterBaseI.pm
|
|
BioPerl-1.007001/Bio/Perl.pm
|
|
BioPerl-1.007001/Bio/PhyloNetwork.pm
|
|
BioPerl-1.007001/Bio/PrimarySeq.pm
|
|
BioPerl-1.007001/Bio/PrimarySeqI.pm
|
|
BioPerl-1.007001/Bio/PullParserI.pm
|
|
BioPerl-1.007001/Bio/Range.pm
|
|
BioPerl-1.007001/Bio/RangeI.pm
|
|
BioPerl-1.007001/Bio/SearchDist.pm
|
|
BioPerl-1.007001/Bio/SearchIO.pm
|
|
BioPerl-1.007001/Bio/Seq.pm
|
|
BioPerl-1.007001/Bio/SeqAnalysisParserI.pm
|
|
BioPerl-1.007001/Bio/SeqFeatureI.pm
|
|
BioPerl-1.007001/Bio/SeqI.pm
|
|
BioPerl-1.007001/Bio/SeqIO.pm
|
|
BioPerl-1.007001/Bio/SeqUtils.pm
|
|
BioPerl-1.007001/Bio/SimpleAlign.pm
|
|
BioPerl-1.007001/Bio/SimpleAnalysisI.pm
|
|
BioPerl-1.007001/Bio/Species.pm
|
|
BioPerl-1.007001/Bio/Taxon.pm
|
|
BioPerl-1.007001/Bio/Taxonomy.pm
|
|
BioPerl-1.007001/Bio/TreeIO.pm
|
|
BioPerl-1.007001/Bio/UpdateableSeqI.pm
|
|
BioPerl-1.007001/Bio/WebAgent.pm
|
|
BioPerl-1.007001/Bio/Align
|
|
BioPerl-1.007001/Bio/Align/AlignI.pm
|
|
BioPerl-1.007001/Bio/Align/DNAStatistics.pm
|
|
BioPerl-1.007001/Bio/Align/Graphics.pm
|
|
BioPerl-1.007001/Bio/Align/PairwiseStatistics.pm
|
|
BioPerl-1.007001/Bio/Align/ProteinStatistics.pm
|
|
BioPerl-1.007001/Bio/Align/StatisticsI.pm
|
|
BioPerl-1.007001/Bio/Align/Utilities.pm
|
|
BioPerl-1.007001/Bio/AlignIO
|
|
BioPerl-1.007001/Bio/AlignIO/arp.pm
|
|
BioPerl-1.007001/Bio/AlignIO/bl2seq.pm
|
|
BioPerl-1.007001/Bio/AlignIO/clustalw.pm
|
|
BioPerl-1.007001/Bio/AlignIO/emboss.pm
|
|
BioPerl-1.007001/Bio/AlignIO/fasta.pm
|
|
BioPerl-1.007001/Bio/AlignIO/largemultifasta.pm
|
|
BioPerl-1.007001/Bio/AlignIO/maf.pm
|
|
BioPerl-1.007001/Bio/AlignIO/mase.pm
|
|
BioPerl-1.007001/Bio/AlignIO/mega.pm
|
|
BioPerl-1.007001/Bio/AlignIO/meme.pm
|
|
BioPerl-1.007001/Bio/AlignIO/metafasta.pm
|
|
BioPerl-1.007001/Bio/AlignIO/msf.pm
|
|
BioPerl-1.007001/Bio/AlignIO/nexml.pm
|
|
BioPerl-1.007001/Bio/AlignIO/nexus.pm
|
|
BioPerl-1.007001/Bio/AlignIO/pfam.pm
|
|
BioPerl-1.007001/Bio/AlignIO/phylip.pm
|
|
BioPerl-1.007001/Bio/AlignIO/po.pm
|
|
BioPerl-1.007001/Bio/AlignIO/proda.pm
|
|
BioPerl-1.007001/Bio/AlignIO/prodom.pm
|
|
BioPerl-1.007001/Bio/AlignIO/psi.pm
|
|
BioPerl-1.007001/Bio/AlignIO/selex.pm
|
|
BioPerl-1.007001/Bio/AlignIO/stockholm.pm
|
|
BioPerl-1.007001/Bio/AlignIO/xmfa.pm
|
|
BioPerl-1.007001/Bio/AlignIO/Handler
|
|
BioPerl-1.007001/Bio/AlignIO/Handler/GenericAlignHandler.pm
|
|
BioPerl-1.007001/Bio/Annotation
|
|
BioPerl-1.007001/Bio/Annotation/AnnotationFactory.pm
|
|
BioPerl-1.007001/Bio/Annotation/Collection.pm
|
|
BioPerl-1.007001/Bio/Annotation/Comment.pm
|
|
BioPerl-1.007001/Bio/Annotation/DBLink.pm
|
|
BioPerl-1.007001/Bio/Annotation/OntologyTerm.pm
|
|
BioPerl-1.007001/Bio/Annotation/Reference.pm
|
|
BioPerl-1.007001/Bio/Annotation/Relation.pm
|
|
BioPerl-1.007001/Bio/Annotation/SimpleValue.pm
|
|
BioPerl-1.007001/Bio/Annotation/StructuredValue.pm
|
|
BioPerl-1.007001/Bio/Annotation/TagTree.pm
|
|
BioPerl-1.007001/Bio/Annotation/Target.pm
|
|
BioPerl-1.007001/Bio/Annotation/Tree.pm
|
|
BioPerl-1.007001/Bio/Annotation/TypeManager.pm
|
|
BioPerl-1.007001/Bio/Assembly
|
|
BioPerl-1.007001/Bio/Assembly/Contig.pm
|
|
BioPerl-1.007001/Bio/Assembly/ContigAnalysis.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO.pm
|
|
BioPerl-1.007001/Bio/Assembly/Scaffold.pm
|
|
BioPerl-1.007001/Bio/Assembly/ScaffoldI.pm
|
|
BioPerl-1.007001/Bio/Assembly/Singlet.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO
|
|
BioPerl-1.007001/Bio/Assembly/IO/ace.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO/bowtie.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO/maq.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO/phrap.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO/sam.pm
|
|
BioPerl-1.007001/Bio/Assembly/IO/tigr.pm
|
|
BioPerl-1.007001/Bio/Assembly/Tools
|
|
BioPerl-1.007001/Bio/Assembly/Tools/ContigSpectrum.pm
|
|
BioPerl-1.007001/Bio/Cluster
|
|
BioPerl-1.007001/Bio/Cluster/ClusterFactory.pm
|
|
BioPerl-1.007001/Bio/Cluster/FamilyI.pm
|
|
BioPerl-1.007001/Bio/Cluster/SequenceFamily.pm
|
|
BioPerl-1.007001/Bio/Cluster/UniGene.pm
|
|
BioPerl-1.007001/Bio/Cluster/UniGeneI.pm
|
|
BioPerl-1.007001/Bio/ClusterIO
|
|
BioPerl-1.007001/Bio/ClusterIO/dbsnp.pm
|
|
BioPerl-1.007001/Bio/ClusterIO/unigene.pm
|
|
BioPerl-1.007001/Bio/CodonUsage
|
|
BioPerl-1.007001/Bio/CodonUsage/IO.pm
|
|
BioPerl-1.007001/Bio/CodonUsage/Table.pm
|
|
BioPerl-1.007001/Bio/Das
|
|
BioPerl-1.007001/Bio/Das/FeatureTypeI.pm
|
|
BioPerl-1.007001/Bio/Das/SegmentI.pm
|
|
BioPerl-1.007001/Bio/DB
|
|
BioPerl-1.007001/Bio/DB/Ace.pm
|
|
BioPerl-1.007001/Bio/DB/BioFetch.pm
|
|
BioPerl-1.007001/Bio/DB/CUTG.pm
|
|
BioPerl-1.007001/Bio/DB/DBFetch.pm
|
|
BioPerl-1.007001/Bio/DB/EMBL.pm
|
|
BioPerl-1.007001/Bio/DB/EntrezGene.pm
|
|
BioPerl-1.007001/Bio/DB/Expression.pm
|
|
BioPerl-1.007001/Bio/DB/Failover.pm
|
|
BioPerl-1.007001/Bio/DB/Fasta.pm
|
|
BioPerl-1.007001/Bio/DB/FileCache.pm
|
|
BioPerl-1.007001/Bio/DB/Flat.pm
|
|
BioPerl-1.007001/Bio/DB/GenBank.pm
|
|
BioPerl-1.007001/Bio/DB/GenericWebAgent.pm
|
|
BioPerl-1.007001/Bio/DB/GenPept.pm
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BioPerl-1.007001/Bio/DB/GFF.pm
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BioPerl-1.007001/Bio/DB/HIV.pm
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BioPerl-1.007001/Bio/DB/IndexedBase.pm
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BioPerl-1.007001/Bio/DB/InMemoryCache.pm
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BioPerl-1.007001/Bio/DB/LocationI.pm
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BioPerl-1.007001/Bio/DB/MeSH.pm
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BioPerl-1.007001/Bio/DB/NCBIHelper.pm
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BioPerl-1.007001/Bio/DB/Qual.pm
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BioPerl-1.007001/Bio/DB/QueryI.pm
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BioPerl-1.007001/Bio/DB/RandomAccessI.pm
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BioPerl-1.007001/Bio/DB/ReferenceI.pm
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BioPerl-1.007001/Bio/DB/RefSeq.pm
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BioPerl-1.007001/Bio/DB/Registry.pm
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BioPerl-1.007001/Bio/DB/SeqFeature.pm
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BioPerl-1.007001/Bio/DB/SeqI.pm
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BioPerl-1.007001/Bio/DB/SeqVersion.pm
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BioPerl-1.007001/Bio/DB/SwissProt.pm
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BioPerl-1.007001/Bio/DB/Taxonomy.pm
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BioPerl-1.007001/Bio/DB/TFBS.pm
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BioPerl-1.007001/Bio/DB/Universal.pm
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BioPerl-1.007001/Bio/DB/UpdateableSeqI.pm
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BioPerl-1.007001/Bio/DB/WebDBSeqI.pm
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BioPerl-1.007001/Bio/DB/Expression
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BioPerl-1.007001/Bio/DB/Expression/geo.pm
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BioPerl-1.007001/Bio/DB/Flat
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BioPerl-1.007001/Bio/DB/Flat/BDB.pm
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BioPerl-1.007001/Bio/DB/Flat/BinarySearch.pm
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BioPerl-1.007001/Bio/DB/Flat/BDB
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BioPerl-1.007001/Bio/DB/Flat/BDB/embl.pm
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BioPerl-1.007001/Bio/DB/Flat/BDB/fasta.pm
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BioPerl-1.007001/Bio/DB/Flat/BDB/genbank.pm
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BioPerl-1.007001/Bio/DB/Flat/BDB/swiss.pm
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BioPerl-1.007001/Bio/DB/GFF
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BioPerl-1.007001/Bio/DB/GFF/Aggregator.pm
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BioPerl-1.007001/Bio/DB/GFF/Featname.pm
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BioPerl-1.007001/Bio/DB/GFF/Feature.pm
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BioPerl-1.007001/Bio/DB/GFF/Homol.pm
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BioPerl-1.007001/Bio/DB/GFF/RelSegment.pm
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BioPerl-1.007001/Bio/DB/GFF/Segment.pm
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BioPerl-1.007001/Bio/DB/GFF/Typename.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/ace.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/berkeleydb.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/biofetch.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/memory.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/berkeleydb
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/iterator.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/mysql.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/oracle.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/pg.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/memory
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
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BioPerl-1.007001/Bio/DB/GFF/Adaptor/memory/iterator.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/alignment.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/clone.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/coding.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/gene.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/match.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/none.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/orf.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/processed_transcript.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/so_transcript.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/transcript.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
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BioPerl-1.007001/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
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BioPerl-1.007001/Bio/DB/GFF/Util
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BioPerl-1.007001/Bio/DB/GFF/Util/Binning.pm
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BioPerl-1.007001/Bio/DB/GFF/Util/Rearrange.pm
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BioPerl-1.007001/Bio/DB/HIV
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BioPerl-1.007001/Bio/DB/HIV/HIVAnnotProcessor.pm
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BioPerl-1.007001/Bio/DB/HIV/HIVQueryHelper.pm
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BioPerl-1.007001/Bio/DB/HIV/lanl-schema.xml
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BioPerl-1.007001/Bio/DB/Query
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BioPerl-1.007001/Bio/DB/Query/GenBank.pm
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BioPerl-1.007001/Bio/DB/Query/HIVQuery.pm
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BioPerl-1.007001/Bio/DB/Query/WebQuery.pm
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BioPerl-1.007001/Bio/DB/SeqFeature
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BioPerl-1.007001/Bio/DB/SeqFeature/NormalizedFeature.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/NormalizedFeatureI.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Segment.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/bdb.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/berkeleydb.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/berkeleydb3.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/GFF2Loader.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/GFF3Loader.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/Loader.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/LoadHelper.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/memory.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/DBI
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/DBI/mysql.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/DBI/Pg.pm
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BioPerl-1.007001/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
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BioPerl-1.007001/Bio/DB/SeqVersion
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BioPerl-1.007001/Bio/DB/SeqVersion/gi.pm
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BioPerl-1.007001/Bio/DB/Taxonomy
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BioPerl-1.007001/Bio/DB/Taxonomy/entrez.pm
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BioPerl-1.007001/Bio/DB/Taxonomy/flatfile.pm
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BioPerl-1.007001/Bio/DB/Taxonomy/greengenes.pm
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BioPerl-1.007001/Bio/DB/Taxonomy/list.pm
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BioPerl-1.007001/Bio/DB/Taxonomy/silva.pm
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BioPerl-1.007001/Bio/DB/Taxonomy/sqlite.pm
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BioPerl-1.007001/Bio/DB/TFBS
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BioPerl-1.007001/Bio/DB/TFBS/transfac_pro.pm
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BioPerl-1.007001/Bio/Draw
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BioPerl-1.007001/Bio/Draw/Pictogram.pm
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BioPerl-1.007001/Bio/Event
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BioPerl-1.007001/Bio/Event/EventGeneratorI.pm
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BioPerl-1.007001/Bio/Event/EventHandlerI.pm
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BioPerl-1.007001/Bio/Factory
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BioPerl-1.007001/Bio/Factory/AnalysisI.pm
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BioPerl-1.007001/Bio/Factory/ApplicationFactoryI.pm
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BioPerl-1.007001/Bio/Factory/DriverFactory.pm
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BioPerl-1.007001/Bio/Factory/FTLocationFactory.pm
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BioPerl-1.007001/Bio/Factory/LocationFactoryI.pm
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BioPerl-1.007001/Bio/Factory/MapFactoryI.pm
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BioPerl-1.007001/Bio/Factory/ObjectBuilderI.pm
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BioPerl-1.007001/Bio/Factory/ObjectFactory.pm
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BioPerl-1.007001/Bio/Factory/ObjectFactoryI.pm
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BioPerl-1.007001/Bio/Factory/SeqAnalysisParserFactory.pm
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BioPerl-1.007001/Bio/Factory/SeqAnalysisParserFactoryI.pm
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BioPerl-1.007001/Bio/Factory/SequenceFactoryI.pm
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BioPerl-1.007001/Bio/Factory/SequenceProcessorI.pm
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BioPerl-1.007001/Bio/Factory/SequenceStreamI.pm
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BioPerl-1.007001/Bio/Factory/TreeFactoryI.pm
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BioPerl-1.007001/Bio/Index
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BioPerl-1.007001/Bio/Index/Abstract.pm
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BioPerl-1.007001/Bio/Index/AbstractSeq.pm
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BioPerl-1.007001/Bio/Index/Blast.pm
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BioPerl-1.007001/Bio/Index/BlastTable.pm
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BioPerl-1.007001/Bio/Index/EMBL.pm
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BioPerl-1.007001/Bio/Index/Fasta.pm
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BioPerl-1.007001/Bio/Index/Fastq.pm
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BioPerl-1.007001/Bio/Index/GenBank.pm
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BioPerl-1.007001/Bio/Index/Hmmer.pm
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BioPerl-1.007001/Bio/Index/Qual.pm
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BioPerl-1.007001/Bio/Index/Stockholm.pm
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BioPerl-1.007001/Bio/Index/SwissPfam.pm
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BioPerl-1.007001/Bio/Index/Swissprot.pm
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BioPerl-1.007001/Bio/LiveSeq
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BioPerl-1.007001/Bio/LiveSeq/AARange.pm
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BioPerl-1.007001/Bio/LiveSeq/Chain.pm
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BioPerl-1.007001/Bio/LiveSeq/ChainI.pm
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BioPerl-1.007001/Bio/LiveSeq/DNA.pm
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BioPerl-1.007001/Bio/LiveSeq/Exon.pm
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BioPerl-1.007001/Bio/LiveSeq/Gene.pm
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BioPerl-1.007001/Bio/LiveSeq/Intron.pm
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BioPerl-1.007001/Bio/LiveSeq/Mutation.pm
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BioPerl-1.007001/Bio/LiveSeq/Mutator.pm
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BioPerl-1.007001/Bio/LiveSeq/Prim_Transcript.pm
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BioPerl-1.007001/Bio/LiveSeq/Range.pm
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BioPerl-1.007001/Bio/LiveSeq/Repeat_Region.pm
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BioPerl-1.007001/Bio/LiveSeq/Repeat_Unit.pm
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BioPerl-1.007001/Bio/LiveSeq/SeqI.pm
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BioPerl-1.007001/Bio/LiveSeq/Transcript.pm
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BioPerl-1.007001/Bio/LiveSeq/Translation.pm
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BioPerl-1.007001/Bio/LiveSeq/IO
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BioPerl-1.007001/Bio/LiveSeq/IO/BioPerl.pm
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BioPerl-1.007001/Bio/LiveSeq/IO/Loader.pm
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BioPerl-1.007001/Bio/LiveSeq/IO/README
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BioPerl-1.007001/Bio/Location
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BioPerl-1.007001/Bio/Location/Atomic.pm
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BioPerl-1.007001/Bio/Location/AvWithinCoordPolicy.pm
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BioPerl-1.007001/Bio/Location/CoordinatePolicyI.pm
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BioPerl-1.007001/Bio/Location/Fuzzy.pm
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BioPerl-1.007001/Bio/Location/FuzzyLocationI.pm
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BioPerl-1.007001/Bio/Location/NarrowestCoordPolicy.pm
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BioPerl-1.007001/Bio/Location/Simple.pm
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BioPerl-1.007001/Bio/Location/Split.pm
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BioPerl-1.007001/Bio/Location/SplitLocationI.pm
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BioPerl-1.007001/Bio/Location/WidestCoordPolicy.pm
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BioPerl-1.007001/Bio/Map
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BioPerl-1.007001/Bio/Map/Clone.pm
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BioPerl-1.007001/Bio/Map/Contig.pm
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BioPerl-1.007001/Bio/Map/CytoMap.pm
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BioPerl-1.007001/Bio/Map/CytoMarker.pm
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BioPerl-1.007001/Bio/Map/CytoPosition.pm
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BioPerl-1.007001/Bio/Map/EntityI.pm
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BioPerl-1.007001/Bio/Map/FPCMarker.pm
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BioPerl-1.007001/Bio/Map/Gene.pm
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BioPerl-1.007001/Bio/Map/GeneMap.pm
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BioPerl-1.007001/Bio/Map/GenePosition.pm
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BioPerl-1.007001/Bio/Map/GeneRelative.pm
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BioPerl-1.007001/Bio/Map/LinkageMap.pm
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BioPerl-1.007001/Bio/Map/LinkagePosition.pm
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BioPerl-1.007001/Bio/Map/MapI.pm
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BioPerl-1.007001/Bio/Map/Mappable.pm
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BioPerl-1.007001/Bio/Map/MappableI.pm
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BioPerl-1.007001/Bio/Map/Marker.pm
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BioPerl-1.007001/Bio/Map/MarkerI.pm
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BioPerl-1.007001/Bio/Map/Microsatellite.pm
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BioPerl-1.007001/Bio/Map/OrderedPosition.pm
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BioPerl-1.007001/Bio/Map/OrderedPositionWithDistance.pm
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BioPerl-1.007001/Bio/Map/Physical.pm
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BioPerl-1.007001/Bio/Map/Position.pm
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BioPerl-1.007001/Bio/Map/PositionHandler.pm
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BioPerl-1.007001/Bio/Map/PositionHandlerI.pm
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BioPerl-1.007001/Bio/Map/PositionI.pm
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BioPerl-1.007001/Bio/Map/PositionWithSequence.pm
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BioPerl-1.007001/Bio/Map/Prediction.pm
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BioPerl-1.007001/Bio/Map/Relative.pm
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BioPerl-1.007001/Bio/Map/RelativeI.pm
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BioPerl-1.007001/Bio/Map/SimpleMap.pm
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BioPerl-1.007001/Bio/Map/TranscriptionFactor.pm
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BioPerl-1.007001/Bio/MapIO
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BioPerl-1.007001/Bio/MapIO/fpc.pm
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BioPerl-1.007001/Bio/MapIO/mapmaker.pm
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BioPerl-1.007001/Bio/Matrix
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BioPerl-1.007001/Bio/Matrix/Generic.pm
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BioPerl-1.007001/Bio/Matrix/IO.pm
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BioPerl-1.007001/Bio/Matrix/MatrixI.pm
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BioPerl-1.007001/Bio/Matrix/Mlagan.pm
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BioPerl-1.007001/Bio/Matrix/PhylipDist.pm
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BioPerl-1.007001/Bio/Matrix/Scoring.pm
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BioPerl-1.007001/Bio/Matrix/IO
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BioPerl-1.007001/Bio/Matrix/IO/mlagan.pm
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BioPerl-1.007001/Bio/Matrix/IO/phylip.pm
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BioPerl-1.007001/Bio/Matrix/IO/scoring.pm
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BioPerl-1.007001/Bio/Matrix/PSM
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BioPerl-1.007001/Bio/Matrix/PSM/InstanceSite.pm
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BioPerl-1.007001/Bio/Matrix/PSM/InstanceSiteI.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO.pm
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BioPerl-1.007001/Bio/Matrix/PSM/ProtMatrix.pm
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BioPerl-1.007001/Bio/Matrix/PSM/ProtPsm.pm
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BioPerl-1.007001/Bio/Matrix/PSM/Psm.pm
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BioPerl-1.007001/Bio/Matrix/PSM/PsmHeader.pm
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BioPerl-1.007001/Bio/Matrix/PSM/PsmHeaderI.pm
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BioPerl-1.007001/Bio/Matrix/PSM/PsmI.pm
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BioPerl-1.007001/Bio/Matrix/PSM/SiteMatrix.pm
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BioPerl-1.007001/Bio/Matrix/PSM/SiteMatrixI.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO
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BioPerl-1.007001/Bio/Matrix/PSM/IO/mast.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO/masta.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO/meme.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO/psiblast.pm
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BioPerl-1.007001/Bio/Matrix/PSM/IO/transfac.pm
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BioPerl-1.007001/Bio/MolEvol
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BioPerl-1.007001/Bio/MolEvol/CodonModel.pm
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BioPerl-1.007001/Bio/Nexml
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BioPerl-1.007001/Bio/Nexml/Factory.pm
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BioPerl-1.007001/Bio/Ontology
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BioPerl-1.007001/Bio/Ontology/DocumentRegistry.pm
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BioPerl-1.007001/Bio/Ontology/GOterm.pm
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BioPerl-1.007001/Bio/Ontology/InterProTerm.pm
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BioPerl-1.007001/Bio/Ontology/OBOEngine.pm
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BioPerl-1.007001/Bio/Ontology/OBOterm.pm
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BioPerl-1.007001/Bio/Ontology/Ontology.pm
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BioPerl-1.007001/Bio/Ontology/OntologyEngineI.pm
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BioPerl-1.007001/Bio/Ontology/OntologyI.pm
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BioPerl-1.007001/Bio/Ontology/OntologyStore.pm
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BioPerl-1.007001/Bio/Ontology/Path.pm
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BioPerl-1.007001/Bio/Ontology/PathI.pm
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BioPerl-1.007001/Bio/Ontology/Relationship.pm
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BioPerl-1.007001/Bio/Ontology/RelationshipFactory.pm
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BioPerl-1.007001/Bio/Ontology/RelationshipI.pm
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BioPerl-1.007001/Bio/Ontology/RelationshipType.pm
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BioPerl-1.007001/Bio/Ontology/SimpleOntologyEngine.pm
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BioPerl-1.007001/Bio/Ontology/Term.pm
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BioPerl-1.007001/Bio/Ontology/TermFactory.pm
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BioPerl-1.007001/Bio/Ontology/TermI.pm
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BioPerl-1.007001/Bio/Ontology/SimpleGOEngine
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BioPerl-1.007001/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
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BioPerl-1.007001/Bio/OntologyIO
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BioPerl-1.007001/Bio/OntologyIO/dagflat.pm
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BioPerl-1.007001/Bio/OntologyIO/goflat.pm
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BioPerl-1.007001/Bio/OntologyIO/InterProParser.pm
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BioPerl-1.007001/Bio/OntologyIO/obo.pm
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BioPerl-1.007001/Bio/OntologyIO/simplehierarchy.pm
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BioPerl-1.007001/Bio/OntologyIO/soflat.pm
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BioPerl-1.007001/Bio/OntologyIO/Handlers
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BioPerl-1.007001/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
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BioPerl-1.007001/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
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BioPerl-1.007001/Bio/OntologyIO/Handlers/InterProHandler.pm
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BioPerl-1.007001/Bio/Phenotype
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BioPerl-1.007001/Bio/Phenotype/Correlate.pm
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BioPerl-1.007001/Bio/Phenotype/Measure.pm
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BioPerl-1.007001/Bio/Phenotype/Phenotype.pm
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BioPerl-1.007001/Bio/Phenotype/PhenotypeI.pm
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BioPerl-1.007001/Bio/Phenotype/MeSH
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BioPerl-1.007001/Bio/Phenotype/MeSH/Term.pm
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BioPerl-1.007001/Bio/Phenotype/MeSH/Twig.pm
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BioPerl-1.007001/Bio/Phenotype/OMIM
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BioPerl-1.007001/Bio/Phenotype/OMIM/MiniMIMentry.pm
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BioPerl-1.007001/Bio/Phenotype/OMIM/OMIMentry.pm
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BioPerl-1.007001/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
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BioPerl-1.007001/Bio/Phenotype/OMIM/OMIMparser.pm
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BioPerl-1.007001/Bio/PhyloNetwork
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BioPerl-1.007001/Bio/PhyloNetwork/Factory.pm
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BioPerl-1.007001/Bio/PhyloNetwork/FactoryX.pm
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BioPerl-1.007001/Bio/PhyloNetwork/GraphViz.pm
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BioPerl-1.007001/Bio/PhyloNetwork/muVector.pm
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BioPerl-1.007001/Bio/PhyloNetwork/RandomFactory.pm
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BioPerl-1.007001/Bio/PhyloNetwork/TreeFactory.pm
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BioPerl-1.007001/Bio/PhyloNetwork/TreeFactoryMulti.pm
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BioPerl-1.007001/Bio/PhyloNetwork/TreeFactoryX.pm
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BioPerl-1.007001/Bio/PopGen
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BioPerl-1.007001/Bio/PopGen/Genotype.pm
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BioPerl-1.007001/Bio/PopGen/GenotypeI.pm
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BioPerl-1.007001/Bio/PopGen/HtSNP.pm
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BioPerl-1.007001/Bio/PopGen/Individual.pm
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BioPerl-1.007001/Bio/PopGen/IndividualI.pm
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BioPerl-1.007001/Bio/PopGen/IO.pm
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BioPerl-1.007001/Bio/PopGen/Marker.pm
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BioPerl-1.007001/Bio/PopGen/MarkerI.pm
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BioPerl-1.007001/Bio/PopGen/PopStats.pm
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BioPerl-1.007001/Bio/PopGen/Population.pm
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BioPerl-1.007001/Bio/PopGen/PopulationI.pm
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BioPerl-1.007001/Bio/PopGen/Statistics.pm
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BioPerl-1.007001/Bio/PopGen/TagHaplotype.pm
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BioPerl-1.007001/Bio/PopGen/Utilities.pm
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BioPerl-1.007001/Bio/PopGen/IO
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BioPerl-1.007001/Bio/PopGen/IO/csv.pm
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BioPerl-1.007001/Bio/PopGen/IO/hapmap.pm
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BioPerl-1.007001/Bio/PopGen/IO/phase.pm
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BioPerl-1.007001/Bio/PopGen/IO/prettybase.pm
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BioPerl-1.007001/Bio/PopGen/Simulation
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BioPerl-1.007001/Bio/PopGen/Simulation/Coalescent.pm
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BioPerl-1.007001/Bio/PopGen/Simulation/GeneticDrift.pm
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BioPerl-1.007001/Bio/Restriction
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BioPerl-1.007001/Bio/Restriction/Analysis.pm
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BioPerl-1.007001/Bio/Restriction/Enzyme.pm
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BioPerl-1.007001/Bio/Restriction/EnzymeCollection.pm
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BioPerl-1.007001/Bio/Restriction/EnzymeI.pm
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BioPerl-1.007001/Bio/Restriction/IO.pm
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BioPerl-1.007001/Bio/Restriction/Enzyme
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BioPerl-1.007001/Bio/Restriction/Enzyme/MultiCut.pm
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BioPerl-1.007001/Bio/Restriction/Enzyme/MultiSite.pm
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BioPerl-1.007001/Bio/Restriction/IO
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BioPerl-1.007001/Bio/Restriction/IO/bairoch.pm
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BioPerl-1.007001/Bio/Restriction/IO/base.pm
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BioPerl-1.007001/Bio/Restriction/IO/itype2.pm
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BioPerl-1.007001/Bio/Restriction/IO/prototype.pm
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BioPerl-1.007001/Bio/Restriction/IO/withrefm.pm
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BioPerl-1.007001/Bio/Root
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BioPerl-1.007001/Bio/Root/Build.pm
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BioPerl-1.007001/Bio/Root/Exception.pm
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BioPerl-1.007001/Bio/Root/HTTPget.pm
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BioPerl-1.007001/Bio/Root/IO.pm
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BioPerl-1.007001/Bio/Root/Root.pm
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BioPerl-1.007001/Bio/Root/Storable.pm
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BioPerl-1.007001/Bio/Root/Test.pm
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BioPerl-1.007001/Bio/Root/TestObject.pm
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BioPerl-1.007001/Bio/Root/Utilities.pm
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BioPerl-1.007001/Bio/Root/Version.pm
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BioPerl-1.007001/Bio/Search
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BioPerl-1.007001/Bio/Search/BlastStatistics.pm
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BioPerl-1.007001/Bio/Search/BlastUtils.pm
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BioPerl-1.007001/Bio/Search/DatabaseI.pm
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BioPerl-1.007001/Bio/Search/GenericDatabase.pm
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BioPerl-1.007001/Bio/Search/GenericStatistics.pm
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BioPerl-1.007001/Bio/Search/Processor.pm
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BioPerl-1.007001/Bio/Search/SearchUtils.pm
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BioPerl-1.007001/Bio/Search/StatisticsI.pm
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BioPerl-1.007001/Bio/Search/Hit
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BioPerl-1.007001/Bio/Search/Hit/BlastHit.pm
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BioPerl-1.007001/Bio/Search/Hit/BlastPullHit.pm
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BioPerl-1.007001/Bio/Search/Hit/Fasta.pm
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BioPerl-1.007001/Bio/Search/Hit/GenericHit.pm
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BioPerl-1.007001/Bio/Search/Hit/HitFactory.pm
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BioPerl-1.007001/Bio/Search/Hit/hmmer3Hit.pm
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BioPerl-1.007001/Bio/Search/Hit/ModelHit.pm
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BioPerl-1.007001/Bio/Search/Hit/PsiBlastHit.pm
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BioPerl-1.007001/Bio/Search/Hit/PullHitI.pm
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BioPerl-1.007001/Bio/Search/HSP
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BioPerl-1.007001/Bio/Search/HSP/BlastHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/BlastPullHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/FastaHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/GenericHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/HMMERHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/HmmpfamHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/HSPFactory.pm
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BioPerl-1.007001/Bio/Search/HSP/HSPI.pm
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BioPerl-1.007001/Bio/Search/HSP/ModelHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/PsiBlastHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/PSLHSP.pm
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BioPerl-1.007001/Bio/Search/HSP/PullHSPI.pm
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BioPerl-1.007001/Bio/Search/HSP/WABAHSP.pm
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BioPerl-1.007001/Bio/Search/Iteration/GenericIteration.pm
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BioPerl-1.007001/Bio/Search/Iteration/IterationI.pm
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BioPerl-1.007001/Bio/Search/Result
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BioPerl-1.007001/Bio/Search/Result/BlastPullResult.pm
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BioPerl-1.007001/Bio/Search/Result/BlastResult.pm
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BioPerl-1.007001/Bio/Search/Result/CrossMatchResult.pm
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BioPerl-1.007001/Bio/Search/Result/GenericResult.pm
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BioPerl-1.007001/Bio/Search/Result/hmmer3Result.pm
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BioPerl-1.007001/Bio/Search/Result/HMMERResult.pm
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BioPerl-1.007001/Bio/Search/Result/HmmpfamResult.pm
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BioPerl-1.007001/Bio/Search/Result/INFERNALResult.pm
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BioPerl-1.007001/Bio/Search/Result/PullResultI.pm
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BioPerl-1.007001/Bio/Search/Result/ResultFactory.pm
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BioPerl-1.007001/Bio/Search/Result/ResultI.pm
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BioPerl-1.007001/Bio/Search/Result/WABAResult.pm
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BioPerl-1.007001/Bio/Search/Tiling
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BioPerl-1.007001/Bio/Search/Tiling/MapTileUtils.pm
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BioPerl-1.007001/Bio/Search/Tiling/MapTiling.pm
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BioPerl-1.007001/Bio/Search/Tiling/TilingI.pm
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BioPerl-1.007001/Bio/SearchIO
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BioPerl-1.007001/Bio/SearchIO/axt.pm
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BioPerl-1.007001/Bio/SearchIO/blast.pm
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BioPerl-1.007001/Bio/SearchIO/blast_pull.pm
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BioPerl-1.007001/Bio/SearchIO/blasttable.pm
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BioPerl-1.007001/Bio/SearchIO/cross_match.pm
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BioPerl-1.007001/Bio/SearchIO/erpin.pm
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BioPerl-1.007001/Bio/SearchIO/EventHandlerI.pm
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BioPerl-1.007001/Bio/SearchIO/exonerate.pm
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BioPerl-1.007001/Bio/SearchIO/fasta.pm
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BioPerl-1.007001/Bio/SearchIO/FastHitEventBuilder.pm
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BioPerl-1.007001/Bio/SearchIO/gmap_f9.pm
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BioPerl-1.007001/Bio/SearchIO/hmmer.pm
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BioPerl-1.007001/Bio/SearchIO/hmmer2.pm
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BioPerl-1.007001/Bio/SearchIO/hmmer3.pm
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BioPerl-1.007001/Bio/SearchIO/hmmer_pull.pm
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BioPerl-1.007001/Bio/SearchIO/infernal.pm
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BioPerl-1.007001/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
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BioPerl-1.007001/Bio/SearchIO/megablast.pm
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BioPerl-1.007001/Bio/SearchIO/psl.pm
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BioPerl-1.007001/Bio/SearchIO/rnamotif.pm
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BioPerl-1.007001/Bio/SearchIO/SearchResultEventBuilder.pm
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BioPerl-1.007001/Bio/SearchIO/SearchWriterI.pm
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BioPerl-1.007001/Bio/SearchIO/sim4.pm
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BioPerl-1.007001/Bio/SearchIO/waba.pm
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BioPerl-1.007001/Bio/SearchIO/wise.pm
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BioPerl-1.007001/Bio/SearchIO/Writer
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BioPerl-1.007001/Bio/SearchIO/Writer/GbrowseGFF.pm
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BioPerl-1.007001/Bio/SearchIO/Writer/HitTableWriter.pm
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BioPerl-1.007001/Bio/SearchIO/Writer/HSPTableWriter.pm
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BioPerl-1.007001/Bio/SearchIO/Writer/HTMLResultWriter.pm
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BioPerl-1.007001/Bio/SearchIO/Writer/ResultTableWriter.pm
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BioPerl-1.007001/Bio/SearchIO/Writer/TextResultWriter.pm
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BioPerl-1.007001/Bio/Seq
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BioPerl-1.007001/Bio/Seq/BaseSeqProcessor.pm
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BioPerl-1.007001/Bio/Seq/EncodedSeq.pm
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BioPerl-1.007001/Bio/Seq/LargeLocatableSeq.pm
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BioPerl-1.007001/Bio/Seq/LargePrimarySeq.pm
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BioPerl-1.007001/Bio/Seq/LargeSeq.pm
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BioPerl-1.007001/Bio/Seq/LargeSeqI.pm
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BioPerl-1.007001/Bio/Seq/Meta.pm
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BioPerl-1.007001/Bio/Seq/MetaI.pm
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BioPerl-1.007001/Bio/Seq/PrimaryQual.pm
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BioPerl-1.007001/Bio/Seq/PrimedSeq.pm
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BioPerl-1.007001/Bio/Seq/QualI.pm
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BioPerl-1.007001/Bio/Seq/Quality.pm
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BioPerl-1.007001/Bio/Seq/RichSeq.pm
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BioPerl-1.007001/Bio/Seq/RichSeqI.pm
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BioPerl-1.007001/Bio/Seq/SeqBuilder.pm
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BioPerl-1.007001/Bio/Seq/SeqFactory.pm
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BioPerl-1.007001/Bio/Seq/SeqFastaSpeedFactory.pm
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BioPerl-1.007001/Bio/Seq/SequenceTrace.pm
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BioPerl-1.007001/Bio/Seq/SeqWithQuality.pm
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BioPerl-1.007001/Bio/Seq/SimulatedRead.pm
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BioPerl-1.007001/Bio/Seq/TraceI.pm
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BioPerl-1.007001/Bio/Seq/Meta
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BioPerl-1.007001/Bio/Seq/Meta/Array.pm
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BioPerl-1.007001/Bio/SeqEvolution
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BioPerl-1.007001/Bio/SeqEvolution/DNAPoint.pm
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BioPerl-1.007001/Bio/SeqEvolution/EvolutionI.pm
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BioPerl-1.007001/Bio/SeqEvolution/Factory.pm
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BioPerl-1.007001/Bio/SeqFeature
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BioPerl-1.007001/Bio/SeqFeature/Amplicon.pm
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BioPerl-1.007001/Bio/SeqFeature/AnnotationAdaptor.pm
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BioPerl-1.007001/Bio/SeqFeature/Collection.pm
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BioPerl-1.007001/Bio/SeqFeature/CollectionI.pm
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BioPerl-1.007001/Bio/SeqFeature/Computation.pm
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BioPerl-1.007001/Bio/SeqFeature/FeaturePair.pm
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BioPerl-1.007001/Bio/SeqFeature/Generic.pm
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BioPerl-1.007001/Bio/SeqFeature/Lite.pm
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BioPerl-1.007001/Bio/SeqFeature/PositionProxy.pm
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BioPerl-1.007001/Bio/SeqFeature/Primer.pm
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BioPerl-1.007001/Bio/SeqFeature/Similarity.pm
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BioPerl-1.007001/Bio/SeqFeature/SimilarityPair.pm
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BioPerl-1.007001/Bio/SeqFeature/SubSeq.pm
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BioPerl-1.007001/Bio/SeqFeature/TypedSeqFeatureI.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene
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BioPerl-1.007001/Bio/SeqFeature/Gene/Exon.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/ExonI.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/GeneStructure.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/GeneStructureI.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/Intron.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/NC_Feature.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/Poly_A_site.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/Promoter.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/Transcript.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/TranscriptI.pm
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BioPerl-1.007001/Bio/SeqFeature/Gene/UTR.pm
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BioPerl-1.007001/Bio/SeqFeature/SiRNA
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BioPerl-1.007001/Bio/SeqFeature/SiRNA/Oligo.pm
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BioPerl-1.007001/Bio/SeqFeature/SiRNA/Pair.pm
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BioPerl-1.007001/Bio/SeqFeature/Tools
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BioPerl-1.007001/Bio/SeqFeature/Tools/FeatureNamer.pm
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BioPerl-1.007001/Bio/SeqFeature/Tools/IDHandler.pm
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BioPerl-1.007001/Bio/SeqFeature/Tools/TypeMapper.pm
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BioPerl-1.007001/Bio/SeqFeature/Tools/Unflattener.pm
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BioPerl-1.007001/Bio/SeqIO
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BioPerl-1.007001/Bio/SeqIO/abi.pm
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BioPerl-1.007001/Bio/SeqIO/ace.pm
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BioPerl-1.007001/Bio/SeqIO/agave.pm
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BioPerl-1.007001/Bio/SeqIO/alf.pm
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BioPerl-1.007001/Bio/SeqIO/asciitree.pm
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BioPerl-1.007001/Bio/SeqIO/bsml.pm
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BioPerl-1.007001/Bio/SeqIO/bsml_sax.pm
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BioPerl-1.007001/Bio/SeqIO/chadoxml.pm
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BioPerl-1.007001/Bio/SeqIO/chaos.pm
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BioPerl-1.007001/Bio/SeqIO/chaosxml.pm
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BioPerl-1.007001/Bio/SeqIO/ctf.pm
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BioPerl-1.007001/Bio/SeqIO/embl.pm
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BioPerl-1.007001/Bio/SeqIO/embldriver.pm
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BioPerl-1.007001/Bio/SeqIO/entrezgene.pm
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BioPerl-1.007001/Bio/SeqIO/excel.pm
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BioPerl-1.007001/Bio/SeqIO/exp.pm
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BioPerl-1.007001/Bio/SeqIO/fasta.pm
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BioPerl-1.007001/Bio/SeqIO/fastq.pm
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BioPerl-1.007001/Bio/SeqIO/flybase_chadoxml.pm
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BioPerl-1.007001/Bio/SeqIO/FTHelper.pm
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BioPerl-1.007001/Bio/SeqIO/game.pm
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BioPerl-1.007001/Bio/SeqIO/gbdriver.pm
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BioPerl-1.007001/Bio/SeqIO/gbxml.pm
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BioPerl-1.007001/Bio/SeqIO/gcg.pm
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BioPerl-1.007001/Bio/SeqIO/genbank.pm
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BioPerl-1.007001/Bio/SeqIO/interpro.pm
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BioPerl-1.007001/Bio/SeqIO/kegg.pm
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BioPerl-1.007001/Bio/SeqIO/largefasta.pm
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BioPerl-1.007001/Bio/SeqIO/lasergene.pm
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BioPerl-1.007001/Bio/SeqIO/locuslink.pm
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BioPerl-1.007001/Bio/SeqIO/mbsout.pm
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BioPerl-1.007001/Bio/SeqIO/metafasta.pm
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BioPerl-1.007001/Bio/SeqIO/msout.pm
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BioPerl-1.007001/Bio/SeqIO/MultiFile.pm
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BioPerl-1.007001/Bio/SeqIO/nexml.pm
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BioPerl-1.007001/Bio/SeqIO/phd.pm
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BioPerl-1.007001/Bio/SeqIO/pir.pm
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BioPerl-1.007001/Bio/SeqIO/pln.pm
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BioPerl-1.007001/Bio/SeqIO/qual.pm
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BioPerl-1.007001/Bio/SeqIO/raw.pm
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BioPerl-1.007001/Bio/SeqIO/scf.pm
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BioPerl-1.007001/Bio/SeqIO/seqxml.pm
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BioPerl-1.007001/Bio/SeqIO/strider.pm
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BioPerl-1.007001/Bio/SeqIO/swiss.pm
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BioPerl-1.007001/Bio/SeqIO/swissdriver.pm
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BioPerl-1.007001/Bio/SeqIO/tab.pm
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BioPerl-1.007001/Bio/SeqIO/table.pm
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BioPerl-1.007001/Bio/SeqIO/tigr.pm
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BioPerl-1.007001/Bio/SeqIO/tigrxml.pm
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BioPerl-1.007001/Bio/SeqIO/tinyseq.pm
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BioPerl-1.007001/Bio/SeqIO/ztr.pm
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BioPerl-1.007001/Bio/SeqIO/game
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BioPerl-1.007001/Bio/SeqIO/game/featHandler.pm
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BioPerl-1.007001/Bio/SeqIO/game/gameHandler.pm
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BioPerl-1.007001/Bio/SeqIO/game/gameSubs.pm
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BioPerl-1.007001/Bio/SeqIO/game/gameWriter.pm
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BioPerl-1.007001/Bio/SeqIO/game/seqHandler.pm
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BioPerl-1.007001/Bio/SeqIO/Handler
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BioPerl-1.007001/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
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BioPerl-1.007001/Bio/SeqIO/tinyseq
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BioPerl-1.007001/Bio/SeqIO/tinyseq/tinyseqHandler.pm
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BioPerl-1.007001/Bio/Structure
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BioPerl-1.007001/Bio/Structure/Atom.pm
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BioPerl-1.007001/Bio/Structure/Chain.pm
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BioPerl-1.007001/Bio/Structure/Entry.pm
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BioPerl-1.007001/Bio/Structure/IO.pm
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BioPerl-1.007001/Bio/Structure/Model.pm
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BioPerl-1.007001/Bio/Structure/Residue.pm
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BioPerl-1.007001/Bio/Structure/StructureI.pm
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BioPerl-1.007001/Bio/Structure/IO
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BioPerl-1.007001/Bio/Structure/IO/pdb.pm
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BioPerl-1.007001/Bio/Structure/SecStr
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BioPerl-1.007001/Bio/Structure/SecStr/DSSP
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BioPerl-1.007001/Bio/Structure/SecStr/DSSP/Res.pm
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BioPerl-1.007001/Bio/Structure/SecStr/STRIDE
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BioPerl-1.007001/Bio/Structure/SecStr/STRIDE/Res.pm
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BioPerl-1.007001/Bio/Symbol
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BioPerl-1.007001/Bio/Symbol/Alphabet.pm
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BioPerl-1.007001/Bio/Symbol/DNAAlphabet.pm
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BioPerl-1.007001/Bio/Symbol/ProteinAlphabet.pm
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BioPerl-1.007001/Bio/Symbol/README.Symbol
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BioPerl-1.007001/Bio/Symbol/Symbol.pm
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BioPerl-1.007001/deobfuscator/Deobfuscator/Build.PL
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BioPerl-1.007001/deobfuscator/Deobfuscator/LICENSE
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BioPerl-1.007001/deobfuscator/Deobfuscator/Makefile.PL
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BioPerl-1.007001/deobfuscator/Deobfuscator/bin/deob_index.pl
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BioPerl-1.007001/examples
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BioPerl-1.007001/examples/bioperl.pl
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BioPerl-1.007001/examples/generate_random_seq.pl
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BioPerl-1.007001/examples/longorf.pl
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BioPerl-1.007001/examples/make_primers.pl
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BioPerl-1.007001/examples/rev_and_trans.pl
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BioPerl-1.007001/examples/align
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BioPerl-1.007001/examples/align/align_on_codons.pl
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BioPerl-1.007001/examples/align/aligntutorial.pl
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BioPerl-1.007001/examples/align/clustalw.pl
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BioPerl-1.007001/examples/align/simplealign.pl
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BioPerl-1.007001/examples/Bio-DB-GFF/load_ucsc.pl
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BioPerl-1.007001/examples/cluster
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BioPerl-1.007001/examples/cluster/dbsnp.pl
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BioPerl-1.007001/examples/contributed
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BioPerl-1.007001/examples/contributed/nmrpdb_parse.pl
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BioPerl-1.007001/examples/contributed/prosite2perl.pl
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BioPerl-1.007001/examples/contributed/rebase2list.pl
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BioPerl-1.007001/examples/db
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BioPerl-1.007001/examples/db/dbfetch
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BioPerl-1.007001/examples/db/est_tissue_query.pl
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BioPerl-1.007001/examples/db/gb2features.pl
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BioPerl-1.007001/examples/db/get_seqs.pl
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BioPerl-1.007001/examples/db/getGenBank.pl
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BioPerl-1.007001/examples/db/rfetch.pl
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BioPerl-1.007001/examples/db/use_registry.pl
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BioPerl-1.007001/examples/liveseq
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BioPerl-1.007001/examples/liveseq/change_gene.pl
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BioPerl-1.007001/examples/popgen
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BioPerl-1.007001/examples/popgen/parse_calc_stats.pl
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BioPerl-1.007001/examples/quality
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BioPerl-1.007001/examples/quality/svgtrace.pl
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BioPerl-1.007001/examples/root
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BioPerl-1.007001/examples/root/exceptions1.pl
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BioPerl-1.007001/examples/root/exceptions3.pl
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BioPerl-1.007001/examples/root/exceptions4.pl
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BioPerl-1.007001/examples/root/README
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BioPerl-1.007001/examples/searchio
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BioPerl-1.007001/examples/searchio/blast_example.pl
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BioPerl-1.007001/examples/searchio/custom_writer.pl
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BioPerl-1.007001/examples/searchio/hspwriter.pl
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BioPerl-1.007001/examples/searchio/psiblast_iterations.pl
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BioPerl-1.007001/examples/searchio/rawwriter.pl
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BioPerl-1.007001/examples/searchio/waba2gff.pl
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BioPerl-1.007001/examples/searchio/waba2gff3.pl
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BioPerl-1.007001/examples/sirna
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BioPerl-1.007001/examples/sirna/rnai_finder.cgi
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BioPerl-1.007001/examples/sirna/TAG
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BioPerl-1.007001/examples/structure
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BioPerl-1.007001/examples/structure/structure-io.pl
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BioPerl-1.007001/examples/tk/gsequence.pl
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BioPerl-1.007001/examples/tk/hitdisplay.pl
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BioPerl-1.007001/examples/tools
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BioPerl-1.007001/examples/tools/extract_genes.pl
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BioPerl-1.007001/examples/tools/gb_to_gff.pl
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BioPerl-1.007001/examples/tools/gff2ps.pl
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BioPerl-1.007001/examples/tools/parse_codeml.pl
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BioPerl-1.007001/examples/tools/psw.pl
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BioPerl-1.007001/examples/tools/reverse-translate.pl
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BioPerl-1.007001/examples/tools/run_genscan.pl
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BioPerl-1.007001/examples/tools/run_primer3.pl
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BioPerl-1.007001/examples/tools/seq_pattern.pl
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BioPerl-1.007001/examples/tools/standaloneblast.pl
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BioPerl-1.007001/examples/tree
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BioPerl-1.007001/examples/tree/paup2phylip.pl
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BioPerl-1.007001/ide/bioperl.komodo
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BioPerl-1.007001/ide/bioperl-mode
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BioPerl-1.007001/ide/bioperl-mode/README
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BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar.md5
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BioPerl-1.007001/ide/bioperl-mode/dist/Changes
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BioPerl-1.007001/ide/bioperl-mode/dist/package-me
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BioPerl-1.007001/maintenance/authors.pl
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BioPerl-1.007001/maintenance/check_URLs.pl
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BioPerl-1.007001/maintenance/cvs2cl_by_file.pl
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BioPerl-1.007001/maintenance/find_mod_deps.pl
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BioPerl-1.007001/maintenance/ncbi_blast_switches.pl
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BioPerl-1.007001/maintenance/pod.pl
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BioPerl-1.007001/maintenance/README
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BioPerl-1.007001/maintenance/version.pl
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BioPerl-1.007001/models/biblio.dia
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BioPerl-1.007001/models/bio_liveseq_variation.dia
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BioPerl-1.007001/models/bio_map.dia
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BioPerl-1.007001/models/bio_restriction.dia
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BioPerl-1.007001/models/bioperl.dia
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BioPerl-1.007001/models/coordinatemapper.dia
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BioPerl-1.007001/models/map_proposal.txt
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BioPerl-1.007001/models/maps_and_markers.dia
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BioPerl-1.007001/models/popgen.dia
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BioPerl-1.007001/models/population_proposal.txt
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BioPerl-1.007001/models/README
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BioPerl-1.007001/scripts
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BioPerl-1.007001/scripts/README
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BioPerl-1.007001/scripts/Bio-DB-GFF
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_generate_histogram.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_meta_gff.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_gadfly.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_wormbase.pl
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BioPerl-1.007001/scripts/Bio-DB-GFF/README
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BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store
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BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
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BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
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BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
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BioPerl-1.007001/scripts/das/bp_das_server.pl
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BioPerl-1.007001/scripts/das/README
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BioPerl-1.007001/scripts/das/TAG
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BioPerl-1.007001/scripts/DB/bp_biofetch_genbank_proxy.pl
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BioPerl-1.007001/scripts/DB/bp_bioflat_index.pl
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BioPerl-1.007001/scripts/DB/bp_biogetseq.pl
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BioPerl-1.007001/scripts/DB/bp_flanks.pl
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BioPerl-1.007001/scripts/DB/TAG
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BioPerl-1.007001/scripts/DB-HIV/bp_hivq.pl
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BioPerl-1.007001/scripts/index
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BioPerl-1.007001/scripts/index/bp_fetch.pl
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BioPerl-1.007001/scripts/index/bp_seqret.pl
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BioPerl-1.007001/scripts/index/TAG
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BioPerl-1.007001/scripts/popgen/bp_composite_LD.pl
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BioPerl-1.007001/scripts/popgen/bp_heterogeneity_test.pl
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BioPerl-1.007001/scripts/searchio/bp_fastam9_to_table.pl
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BioPerl-1.007001/scripts/searchio/bp_filter_search.pl
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BioPerl-1.007001/scripts/searchio/bp_hmmer_to_table.pl
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BioPerl-1.007001/scripts/searchio/bp_parse_hmmsearch.pl
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BioPerl-1.007001/scripts/searchio/bp_search2table.pl
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BioPerl-1.007001/scripts/searchio/README
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BioPerl-1.007001/scripts/searchio/TAG
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BioPerl-1.007001/scripts/seq
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BioPerl-1.007001/scripts/seq/bp_extract_feature_seq.pl
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BioPerl-1.007001/scripts/seq/bp_make_mrna_protein.pl
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BioPerl-1.007001/scripts/seq/bp_seqconvert.pl
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BioPerl-1.007001/scripts/seq/bp_unflatten_seq.pl
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BioPerl-1.007001/scripts/seqstats
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BioPerl-1.007001/scripts/seqstats/bp_aacomp.pl
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BioPerl-1.007001/scripts/seqstats/bp_chaos_plot.pl
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BioPerl-1.007001/scripts/seqstats/bp_gccalc.pl
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BioPerl-1.007001/scripts/seqstats/bp_oligo_count.pl
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BioPerl-1.007001/scripts/seqstats/TAG
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BioPerl-1.007001/scripts/taxa
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BioPerl-1.007001/scripts/taxa/bp_classify_hits_kingdom.pl
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BioPerl-1.007001/scripts/taxa/bp_local_taxonomydb_query.pl
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BioPerl-1.007001/scripts/taxa/bp_query_entrez_taxa.pl
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BioPerl-1.007001/scripts/taxa/bp_taxid4species.pl
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BioPerl-1.007001/scripts/taxa/bp_taxonomy2tree.pl
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BioPerl-1.007001/scripts/taxa/TAG
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BioPerl-1.007001/scripts/tree
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BioPerl-1.007001/scripts/tree/bp_blast2tree.pl
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BioPerl-1.007001/scripts/tree/bp_nexus2nh.pl
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BioPerl-1.007001/scripts/tree/bp_tree2pag.pl
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BioPerl-1.007001/scripts/utilities
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BioPerl-1.007001/scripts/utilities/bp_dbsplit.pl
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BioPerl-1.007001/scripts/utilities/bp_download_query_genbank.pl
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BioPerl-1.007001/scripts/utilities/bp_find-blast-matches.pl
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BioPerl-1.007001/scripts/utilities/bp_mask_by_search.pl
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BioPerl-1.007001/scripts/utilities/bp_mrtrans.pl
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BioPerl-1.007001/scripts/utilities/bp_mutate.pl
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BioPerl-1.007001/scripts/utilities/bp_pairwise_kaks.pl
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BioPerl-1.007001/scripts/utilities/bp_remote_blast.pl
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BioPerl-1.007001/scripts/utilities/bp_revtrans-motif.pl
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BioPerl-1.007001/scripts/utilities/bp_search2alnblocks.pl
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BioPerl-1.007001/scripts/utilities/bp_search2gff.pl
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BioPerl-1.007001/scripts/utilities/bp_seq_length.pl
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BioPerl-1.007001/scripts/utilities/bp_sreformat.pl
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BioPerl-1.007001/scripts/utilities/README
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BioPerl-1.007001/t/Alphabet.t
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BioPerl-1.007001/t/nexml.t
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BioPerl-1.007001/t/Perl.t
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BioPerl-1.007001/t/PodSyntax.t
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BioPerl-1.007001/t/SearchDist.t
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BioPerl-1.007001/t/SeqEvolution.t
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BioPerl-1.007001/t/Species.t
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BioPerl-1.007001/t/Symbol.t
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BioPerl-1.007001/t/TaxonTree.t
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BioPerl-1.007001/t/Align/AlignUtil.t
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BioPerl-1.007001/t/Annotation/AnnotationAdaptor.t
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BioPerl-1.007001/t/Assembly/IO/sam.t
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BioPerl-1.007001/t/ClusterIO/ClusterIO.t
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BioPerl-1.007001/t/ClusterIO/SequenceFamily.t
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BioPerl-1.007001/t/ClusterIO/unigene.t
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BioPerl-1.007001/t/data
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BioPerl-1.007001/t/data/01_basic.xml
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BioPerl-1.007001/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
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BioPerl-1.007001/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
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BioPerl-1.007001/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
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BioPerl-1.007001/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
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BioPerl-1.007001/t/data/13-pilE-F.scf
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BioPerl-1.007001/t/data/1BPT.pdb
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BioPerl-1.007001/t/data/1ZZ19XR301R-Alignment.tblastn
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BioPerl-1.007001/t/data/2008.blasttable
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BioPerl-1.007001/t/data/27-contig_Newbler.ace
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BioPerl-1.007001/t/data/503384.MEGABLAST.0
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BioPerl-1.007001/t/data/503384.MEGABLAST.2
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BioPerl-1.007001/t/data/5X_1895.FASTXY
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BioPerl-1.007001/t/data/8HVP.pdb
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BioPerl-1.007001/t/data/AAC12660.fa
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BioPerl-1.007001/t/data/aaml_pairwise.mlc
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BioPerl-1.007001/t/data/adh.mb_tree.nexus
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BioPerl-1.007001/t/data/AE003528_ecoli.bls
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BioPerl-1.007001/t/data/AE003644_Adh-genomic.gb
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BioPerl-1.007001/t/data/AnnIX-v003.gbk
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BioPerl-1.007001/t/data/assembly_with_singlets.ace
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BioPerl-1.007001/t/data/biofpc.cor
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BioPerl-1.007001/t/data/Bird_Ovomucoids.nex
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BioPerl-1.007001/t/data/BK000016-tpa.gbk
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BioPerl-1.007001/t/data/bl2seq+.blastn
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BioPerl-1.007001/t/data/bl2seq.blastn.rev
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BioPerl-1.007001/t/data/bl2seq.tblastn.out
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BioPerl-1.007001/t/data/bl2seq.tblastx.out
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BioPerl-1.007001/t/data/blast_no_hit_desc.txt
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BioPerl-1.007001/t/data/blast_plus.blastp
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BioPerl-1.007001/t/data/BOSS_DROME.FASTP_v35_04
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BioPerl-1.007001/t/data/branchSite.mlc
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BioPerl-1.007001/t/data/crab.dat.cn
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BioPerl-1.007001/t/data/crab.nj
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BioPerl-1.007001/t/data/crab.njb
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BioPerl-1.007001/t/data/crypto.sim4-0
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BioPerl-1.007001/t/data/crypto.sim4-3
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BioPerl-1.007001/t/data/crypto.sim4-4
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BioPerl-1.007001/t/data/ctgdemo.fpc
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BioPerl-1.007001/t/data/cys1_dicdi.water
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BioPerl-1.007001/t/data/cysprot.fa
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BioPerl-1.007001/t/data/cysprot.msf
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BioPerl-1.007001/t/data/cysprot.needle
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BioPerl-1.007001/t/data/cysprot.tblastn
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BioPerl-1.007001/t/data/cysprot.water
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BioPerl-1.007001/t/data/cysprot1.fa
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BioPerl-1.007001/t/data/cysprot1.FASTA
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BioPerl-1.007001/t/data/cysprot1a.fa
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BioPerl-1.007001/t/data/cysprot1a.msf
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BioPerl-1.007001/t/data/cysprot1b.fa
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BioPerl-1.007001/t/data/cysprot1b.hmmsearch
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BioPerl-1.007001/t/data/cysprot1b.msf
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BioPerl-1.007001/t/data/cysprot1b.newick
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BioPerl-1.007001/t/data/cysprot_vs_gadfly.FASTA
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BioPerl-1.007001/t/data/D10483.gbk
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BioPerl-1.007001/t/data/D12555.gbk
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BioPerl-1.007001/t/data/dcr1_sp.WUBLASTP
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BioPerl-1.007001/t/data/dmel_2Lchunk.gb
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BioPerl-1.007001/t/data/dna1.fa
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BioPerl-1.007001/t/data/dna2.fa
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BioPerl-1.007001/t/data/dnaE-bsub-prot.fa
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BioPerl-1.007001/t/data/dnaE-bsub.fa
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BioPerl-1.007001/t/data/dnaEbsub_ecoli.wublastx
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BioPerl-1.007001/t/data/dnaEbsub_ecoli.wutblastn
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BioPerl-1.007001/t/data/DQ018368.gb
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BioPerl-1.007001/t/data/dq519393.gb
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BioPerl-1.007001/t/data/ECAPAH02.embl
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BioPerl-1.007001/t/data/echofilter.wublastn
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BioPerl-1.007001/t/data/ecoli-trna-qrna.out
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BioPerl-1.007001/t/data/ecoli_domains.rpsblast
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BioPerl-1.007001/t/data/ecolitst.bls
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BioPerl-1.007001/t/data/ecolitst.fa
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BioPerl-1.007001/t/data/ecolitst.noseqs.wublastp
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BioPerl-1.007001/t/data/ecolitst.wublastp
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BioPerl-1.007001/t/data/EG352462.gbxml
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BioPerl-1.007001/t/data/empty.bl2seq
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BioPerl-1.007001/t/data/ENr111.mfa.example.elems
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BioPerl-1.007001/t/data/entrezgene.dat
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BioPerl-1.007001/t/data/entrezgene_bug3453.dat
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BioPerl-1.007001/t/data/ex1.nucl.nhx
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BioPerl-1.007001/t/data/example.hap
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BioPerl-1.007001/t/data/example.phase
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BioPerl-1.007001/t/data/example.vcf
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BioPerl-1.007001/t/data/exonerate.output.dontwork
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BioPerl-1.007001/t/data/exonerate.output.negativescore.works
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BioPerl-1.007001/t/data/exonerate.output.works
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BioPerl-1.007001/t/data/exonerate.whitespace_before_query.works
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BioPerl-1.007001/t/data/expected.blast.out
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BioPerl-1.007001/t/data/exsignalp.out
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BioPerl-1.007001/t/data/factor7.embl
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BioPerl-1.007001/t/data/Fang_2003.xml
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BioPerl-1.007001/t/data/fgenesh.out
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BioPerl-1.007001/t/data/footprinter.out
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BioPerl-1.007001/t/data/forward_primer.fa
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BioPerl-1.007001/t/data/forward_reverse_primers.fa
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BioPerl-1.007001/t/data/frac_problems.blast
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BioPerl-1.007001/t/data/frac_problems2.blast
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BioPerl-1.007001/t/data/frac_problems3.blast
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BioPerl-1.007001/t/data/geneid_1.0.out
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BioPerl-1.007001/t/data/genewise_output.paracel_btk
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BioPerl-1.007001/t/data/genomewise.out
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BioPerl-1.007001/t/data/genomic-seq.epcr
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BioPerl-1.007001/t/data/genomic-seq.fasta
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BioPerl-1.007001/t/data/genomic-seq.genscan
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BioPerl-1.007001/t/data/genomic-seq.mzef
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BioPerl-1.007001/t/data/Genscan.FastA
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BioPerl-1.007001/t/data/gf-s71.needle
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BioPerl-1.007001/t/data/Glimmer2.out
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BioPerl-1.007001/t/data/glimmer3-fragment.detail
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BioPerl-1.007001/t/data/glimmer3-fragment.predict
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BioPerl-1.007001/t/data/Glimmer3.detail
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BioPerl-1.007001/t/data/Glimmer3.predict
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BioPerl-1.007001/t/data/GlimmerHMM.out
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BioPerl-1.007001/t/data/GlimmerM.out
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BioPerl-1.007001/t/data/gmap_f9-multiple_results.txt
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BioPerl-1.007001/t/data/gmap_f9-reverse-strand.txt
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BioPerl-1.007001/t/data/gmap_f9.txt
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BioPerl-1.007001/t/data/GO.defs.test
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BioPerl-1.007001/t/data/GO.defs.test2
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BioPerl-1.007001/t/data/hg16_chroms.gff
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BioPerl-1.007001/t/data/HM138502.gbk
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BioPerl-1.007001/t/data/hmmpfam_HSPdashline.txt
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BioPerl-1.007001/t/data/hmmpfam_multiresult.out
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BioPerl-1.007001/t/data/hmmscan_qry_stop.txt
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BioPerl-1.007001/t/data/hs_fugu.newick
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BioPerl-1.007001/t/data/hs_owlmonkey.fasta
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BioPerl-1.007001/t/data/hsinsulin.blastcl3.blastn
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BioPerl-1.007001/t/data/HUMBETGLOA.fa
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BioPerl-1.007001/t/data/HUMBETGLOA.grail
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BioPerl-1.007001/t/data/HUMBETGLOA.mzef
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BioPerl-1.007001/t/data/HUMBETGLOA.tblastx
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BioPerl-1.007001/t/data/humts1.pal
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BioPerl-1.007001/t/data/hybrid2.gff3
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BioPerl-1.007001/t/data/lucy.qual
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BioPerl-1.007001/t/data/lysozyme6.protml
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BioPerl-1.007001/t/data/lysozyme6.simple.protml
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BioPerl-1.007001/t/data/M0.mlc
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BioPerl-1.007001/t/data/M12730.gb
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BioPerl-1.007001/t/data/mapmaker.out
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BioPerl-1.007001/t/data/mapmaker.txt
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BioPerl-1.007001/t/data/match.output
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BioPerl-1.007001/t/data/megablast_output.paracel_btk
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BioPerl-1.007001/t/data/mini-AE001405.gb
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BioPerl-1.007001/t/data/mixedmast.dat
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BioPerl-1.007001/t/data/MmCT
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BioPerl-1.007001/t/data/MSGEFTUA.gb
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BioPerl-1.007001/t/data/multiline-intrablock-comment.nex
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BioPerl-1.007001/t/data/no_semicolon.newick
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BioPerl-1.007001/t/data/O_sat.wgs
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BioPerl-1.007001/t/data/omim_genemap_test
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BioPerl-1.007001/t/data/P39765.gb
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BioPerl-1.007001/t/data/pfamOutput-bug3376.out
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BioPerl-1.007001/t/data/phi.out
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BioPerl-1.007001/t/data/phipsi.out
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BioPerl-1.007001/t/data/phmmer.out
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BioPerl-1.007001/t/data/phylipdist.out
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BioPerl-1.007001/t/data/psiblastreport.out
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BioPerl-1.007001/t/data/PX1CG.gb
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BioPerl-1.007001/t/data/Q8GBD3.swiss
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BioPerl-1.007001/t/data/short.blx
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BioPerl-1.007001/t/data/singleNSsite.mlc
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BioPerl-1.007001/t/data/spaced_fasta.fa
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BioPerl-1.007001/t/data/map_hem/HEM15.ups.fa_.revcom
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BioPerl-1.007001/t/data/map_hem/HEM2.ups.fa_
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BioPerl-1.007001/t/data/map_hem/HEM2.ups.fa_.revcom
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BioPerl-1.007001/t/data/map_hem/HEM3-HEM13.fa
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BioPerl-1.007001/t/data/map_hem/HEM3-HEM14.meme.txt
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BioPerl-1.007001/t/data/map_hem/HEM3-HEM15.fa
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BioPerl-1.007001/t/data/map_hem/HEM3-HEM15.meme.txt
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BioPerl-1.007001/t/data/map_hem/HEM3.ups.fa_
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BioPerl-1.007001/t/data/map_hem/HEM3.ups.fa_.revcom
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BioPerl-1.007001/t/data/map_hem/HEM4-HEM14.fa
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BioPerl-1.007001/t/data/map_hem/HEM4-HEM14.meme.txt
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BioPerl-1.007001/t/data/map_hem/HEM4-HEM15.fa
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BioPerl-1.007001/t/data/map_hem/HEM4-HEM15.meme.txt
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BioPerl-1.007001/t/data/map_hem/HEM4.ups.fa_
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BioPerl-1.007001/t/data/map_hem/HEM4.ups.fa_.revcom
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BioPerl-1.007001/t/data/map_hem/yeast.nc.1.freq
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BioPerl-1.007001/t/SeqTools/SeqStats.t
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BioPerl-1.007001/t/SeqTools/SeqUtils.t
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BioPerl-1.007001/t/SeqTools/SeqWords.t
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BioPerl-1.007001/t/Structure
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BioPerl-1.007001/t/Structure/IO.t
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BioPerl-1.007001/t/Structure/Structure.t
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BioPerl-1.007001/t/Tools
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BioPerl-1.007001/t/Tools/AmpliconSearch.t
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BioPerl-1.007001/t/Tools/ePCR.t
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BioPerl-1.007001/t/Tools/Est2Genome.t
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BioPerl-1.007001/t/Tools/FootPrinter.t
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BioPerl-1.007001/t/Tools/Geneid.t
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BioPerl-1.007001/t/Tools/Genewise.t
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BioPerl-1.007001/t/Tools/Genomewise.t
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BioPerl-1.007001/t/Tools/Genpred.t
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BioPerl-1.007001/t/Tools/GFF.t
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BioPerl-1.007001/t/Tools/Hmmer.t
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BioPerl-1.007001/t/Tools/IUPAC.t
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BioPerl-1.007001/t/Tools/Lucy.t
|
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BioPerl-1.007001/t/Tools/Match.t
|
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BioPerl-1.007001/t/Tools/pICalculator.t
|
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BioPerl-1.007001/t/Tools/Primer3.t
|
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BioPerl-1.007001/t/Tools/Promoterwise.t
|
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BioPerl-1.007001/t/Tools/Pseudowise.t
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BioPerl-1.007001/t/Tools/QRNA.t
|
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BioPerl-1.007001/t/Tools/RandDistFunctions.t
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BioPerl-1.007001/t/Tools/RepeatMasker.t
|
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BioPerl-1.007001/t/Tools/Seg.t
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BioPerl-1.007001/t/Tools/Sigcleave.t
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BioPerl-1.007001/t/Tools/Signalp.t
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BioPerl-1.007001/t/Tools/Sim4.t
|
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BioPerl-1.007001/t/Tools/SiRNA.t
|
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BioPerl-1.007001/t/Tools/TandemRepeatsFinder.t
|
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BioPerl-1.007001/t/Tools/TargetP.t
|
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BioPerl-1.007001/t/Tools/Tmhmm.t
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BioPerl-1.007001/t/Tools/tRNAscanSE.t
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BioPerl-1.007001/t/Tools/Alignment
|
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BioPerl-1.007001/t/Tools/Alignment/Consed.t
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BioPerl-1.007001/t/Tools/Analysis
|
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BioPerl-1.007001/t/Tools/Analysis/DNA
|
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BioPerl-1.007001/t/Tools/Analysis/DNA/ESEfinder.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/Domcut.t
|
|
BioPerl-1.007001/t/Tools/Analysis/Protein/ELM.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/GOR4.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/HNN.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/NetPhos.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/Scansite.t
|
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BioPerl-1.007001/t/Tools/Analysis/Protein/Sopma.t
|
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BioPerl-1.007001/t/Tools/EMBOSS
|
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BioPerl-1.007001/t/Tools/EMBOSS/Palindrome.t
|
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BioPerl-1.007001/t/Tools/Phylo
|
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BioPerl-1.007001/t/Tools/Phylo/Gerp.t
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BioPerl-1.007001/t/Tools/Phylo/Molphy.t
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BioPerl-1.007001/t/Tools/Phylo/PAML.t
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BioPerl-1.007001/t/Tools/Phylo/Phylip
|
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BioPerl-1.007001/t/Tools/Phylo/Phylip/ProtDist.t
|
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BioPerl-1.007001/t/Tools/Run
|
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BioPerl-1.007001/t/Tools/Run/RemoteBlast.t
|
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BioPerl-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
|
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BioPerl-1.007001/t/Tools/Signalp
|
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BioPerl-1.007001/t/Tools/Signalp/ExtendedSignalp.t
|
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BioPerl-1.007001/t/Tools/Spidey
|
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BioPerl-1.007001/t/Tools/Spidey/Spidey.t
|
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BioPerl-1.007001/t/Tree
|
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BioPerl-1.007001/t/Tree/Compatible.t
|
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BioPerl-1.007001/t/Tree/Node.t
|
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BioPerl-1.007001/t/Tree/RandomTreeFactory.t
|
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BioPerl-1.007001/t/Tree/Tree.t
|
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BioPerl-1.007001/t/Tree/TreeIO.t
|
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BioPerl-1.007001/t/Tree/TreeStatistics.t
|
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BioPerl-1.007001/t/Tree/PhyloNetwork
|
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BioPerl-1.007001/t/Tree/PhyloNetwork/Factory.t
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BioPerl-1.007001/t/Tree/PhyloNetwork/GraphViz.t
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BioPerl-1.007001/t/Tree/PhyloNetwork/MuVector.t
|
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BioPerl-1.007001/t/Tree/PhyloNetwork/PhyloNetwork.t
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BioPerl-1.007001/t/Tree/PhyloNetwork/RandomFactory.t
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BioPerl-1.007001/t/Tree/PhyloNetwork/TreeFactory.t
|
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BioPerl-1.007001/t/Tree/TreeIO
|
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BioPerl-1.007001/t/Tree/TreeIO/lintree.t
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BioPerl-1.007001/t/Tree/TreeIO/newick.t
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BioPerl-1.007001/t/Tree/TreeIO/nexml.t
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BioPerl-1.007001/t/Tree/TreeIO/nexus.t
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BioPerl-1.007001/t/Tree/TreeIO/nhx.t
|
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BioPerl-1.007001/t/Tree/TreeIO/phyloxml.t
|
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BioPerl-1.007001/t/Tree/TreeIO/svggraph.t
|
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BioPerl-1.007001/t/Tree/TreeIO/tabtree.t
|
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BioPerl-1.007001/t/Variation
|
|
BioPerl-1.007001/t/Variation/AAChange.t
|
|
BioPerl-1.007001/t/Variation/AAReverseMutate.t
|
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BioPerl-1.007001/t/Variation/Allele.t
|
|
BioPerl-1.007001/t/Variation/DNAMutation.t
|
|
BioPerl-1.007001/t/Variation/RNAChange.t
|
|
BioPerl-1.007001/t/Variation/SeqDiff.t
|
|
BioPerl-1.007001/t/Variation/SNP.t
|
|
BioPerl-1.007001/t/Variation/Variation_IO.t
|
|
BioPerl-1.007001/travis_scripts
|
|
BioPerl-1.007001/travis_scripts/dependency_installs
|
|
BioPerl-1.007001/travis_scripts/trigger-dockerhub.sh
|
|
Entering BioPerl-1.007001
|
|
Checking configure dependencies from META.json
|
|
Checking if you have Module::Build 0.42 ... Yes (0.4222)
|
|
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
|
|
Running Build.PL
|
|
Configuring BioPerl-1.007001 ... Checking prerequisites...
|
|
recommends:
|
|
* XML::DOM::XPath is not installed
|
|
|
|
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
|
|
of the modules indicated above before proceeding with this installation
|
|
|
|
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests
|
|
|
|
Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
|
|
|
|
Do you want to run tests that require connection to servers across the internet
|
|
(likely to cause some failures)? y/n [n] - will not run internet-requiring tests
|
|
Created MYMETA.yml and MYMETA.json
|
|
Creating new 'Build' script for 'BioPerl' version '1.007001'
|
|
Checking dependencies from MYMETA.json ...
|
|
Checking if you have ExtUtils::Manifest 1.52 ... Yes (1.70)
|
|
Checking if you have Test::Most 0 ... Yes (0.35)
|
|
Checking if you have IO::String 0 ... Yes (1.08)
|
|
Checking if you have Test::Harness 2.62 ... Yes (3.39)
|
|
Checking if you have CPAN 1.81 ... Yes (2.16)
|
|
Checking if you have Data::Stag 0.11 ... Yes (0.14)
|
|
Checking if you have Scalar::Util 0 ... Yes (1.47)
|
|
Checking if you have URI::Escape 0 ... Yes (3.31)
|
|
Checking if you have Module::Build 0.42 ... Yes (0.4222)
|
|
OK
|
|
Building and testing BioPerl-1.007001 ... Building BioPerl
|
|
t/Align/AlignStats.t ................... ok
|
|
t/Align/AlignUtil.t .................... ok
|
|
t/Align/Graphics.t ..................... ok
|
|
t/Align/SimpleAlign.t .................. ok
|
|
t/Align/TreeBuild.t .................... ok
|
|
t/Align/Utilities.t .................... ok
|
|
t/AlignIO/AlignIO.t .................... ok
|
|
t/AlignIO/arp.t ........................ ok
|
|
t/AlignIO/bl2seq.t ..................... ok
|
|
t/AlignIO/clustalw.t ................... ok
|
|
t/AlignIO/emboss.t ..................... ok
|
|
t/AlignIO/fasta.t ...................... ok
|
|
t/AlignIO/largemultifasta.t ............ ok
|
|
t/AlignIO/maf.t ........................ ok
|
|
t/AlignIO/mase.t ....................... ok
|
|
t/AlignIO/mega.t ....................... ok
|
|
t/AlignIO/meme.t ....................... ok
|
|
t/AlignIO/metafasta.t .................. ok
|
|
t/AlignIO/msf.t ........................ ok
|
|
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
|
|
t/AlignIO/nexml.t ...................... ok
|
|
t/AlignIO/nexus.t ...................... ok
|
|
t/AlignIO/pfam.t ....................... ok
|
|
t/AlignIO/phylip.t ..................... ok
|
|
t/AlignIO/po.t ......................... ok
|
|
t/AlignIO/prodom.t ..................... ok
|
|
t/AlignIO/psi.t ........................ ok
|
|
t/AlignIO/selex.t ...................... ok
|
|
t/AlignIO/stockholm.t .................. ok
|
|
t/AlignIO/xmfa.t ....................... ok
|
|
t/Alphabet.t ........................... ok
|
|
t/Annotation/Annotation.t .............. ok
|
|
t/Annotation/AnnotationAdaptor.t ....... ok
|
|
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Echo.pm line 25.
|
|
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Nouse.pm line 28.
|
|
t/Assembly/ContigSpectrum.t ............ ok
|
|
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::Tools::Run::Samtools (or dependencies thereof) was not installed
|
|
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::Tools::Run::Samtools (or dependencies thereof) was not installed
|
|
t/Assembly/core.t ...................... ok
|
|
t/Cluster/UniGene.t .................... ok
|
|
t/ClusterIO/ClusterIO.t ................ ok
|
|
t/ClusterIO/SequenceFamily.t ........... ok
|
|
t/ClusterIO/unigene.t .................. ok
|
|
t/Draw/Pictogram.t ..................... ok
|
|
t/LiveSeq/Chain.t ...................... ok
|
|
t/LiveSeq/LiveSeq.t .................... ok
|
|
t/LiveSeq/Mutation.t ................... ok
|
|
t/LiveSeq/Mutator.t .................... ok
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at Bio/DB/GFF.pm line 2000.
|
|
|
|
You are loading a Bio::DB::GFF database with GFF3 formatted data.
|
|
While this will likely work fine, the Bio::DB::GFF schema does not
|
|
always faithfully capture the complexity represented in GFF3 files.
|
|
Unless you have a specific reason for using Bio::DB::GFF, we suggest
|
|
that you use a Bio::DB::SeqFeature::Store database and its corresponding
|
|
loader, bp_seqfeature_load.pl.
|
|
|
|
t/LocalDB/BioDBGFF.t ................... ok
|
|
Subroutine dl_load_flags redefined at (eval 73) line 8.
|
|
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at (eval 73) line 9.
|
|
t/LocalDB/Fasta.t ...................... ok
|
|
t/LocalDB/Flat.t ....................... ok
|
|
t/LocalDB/Index/Blast.t ................ ok
|
|
t/LocalDB/Index/BlastTable.t ........... ok
|
|
t/LocalDB/Index/Index.t ................ ok
|
|
t/LocalDB/Qual.t ....................... ok
|
|
t/LocalDB/Registry.t ................... ok
|
|
t/LocalDB/SeqFeature.t ................. ok
|
|
t/LocalDB/Taxonomy/greengenes.t ........ ok
|
|
t/LocalDB/Taxonomy/silva.t ............. ok
|
|
t/LocalDB/Taxonomy/sqlite.t ............ ok
|
|
t/LocalDB/transfac_pro.t ............... ok
|
|
t/Map/Cyto.t ........................... ok
|
|
t/Map/Linkage.t ........................ ok
|
|
t/Map/Map.t ............................ ok
|
|
t/Map/MapIO.t .......................... ok
|
|
t/Map/MicrosatelliteMarker.t ........... ok
|
|
t/Map/Physical.t ....................... ok
|
|
t/Matrix/IO/masta.t .................... ok
|
|
t/Matrix/IO/psm.t ...................... ok
|
|
t/Matrix/InstanceSite.t ................ ok
|
|
t/Matrix/Matrix.t ...................... ok
|
|
t/Matrix/ProtMatrix.t .................. ok
|
|
t/Matrix/ProtPsm.t ..................... ok
|
|
t/Matrix/SiteMatrix.t .................. ok
|
|
t/Ontology/GOterm.t .................... ok
|
|
t/Ontology/GraphAdaptor.t .............. ok
|
|
t/Ontology/IO/go.t ..................... ok
|
|
t/Ontology/IO/interpro.t ............... ok
|
|
t/Ontology/IO/obo.t .................... ok
|
|
t/Ontology/Ontology.t .................. ok
|
|
t/Ontology/OntologyEngine.t ............ ok
|
|
t/Ontology/OntologyStore.t ............. skipped: Network tests have not been requested
|
|
t/Ontology/Relationship.t .............. ok
|
|
t/Ontology/RelationshipType.t .......... ok
|
|
t/Ontology/Term.t ...................... ok
|
|
t/Perl.t ............................... ok
|
|
t/Phenotype/Correlate.t ................ ok
|
|
t/Phenotype/MeSH.t ..................... ok
|
|
t/Phenotype/Measure.t .................. ok
|
|
t/Phenotype/MiniMIMentry.t ............. ok
|
|
t/Phenotype/OMIMentry.t ................ ok
|
|
t/Phenotype/OMIMentryAllelicVariant.t .. ok
|
|
t/Phenotype/OMIMparser.t ............... ok
|
|
t/Phenotype/Phenotype.t ................ ok
|
|
t/PodSyntax.t .......................... ok
|
|
t/PopGen/Coalescent.t .................. ok
|
|
t/PopGen/HtSNP.t ....................... ok
|
|
t/PopGen/MK.t .......................... ok
|
|
t/PopGen/PopGen.t ...................... ok
|
|
t/PopGen/PopGenSims.t .................. ok
|
|
t/PopGen/TagHaplotype.t ................ ok
|
|
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
|
|
t/RemoteDB/CUTG.t ...................... ok
|
|
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
|
|
t/RemoteDB/EntrezGene.t ................ skipped: Network tests have not been requested
|
|
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
|
|
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
|
|
t/RemoteDB/HIV/HIV.t ................... ok
|
|
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
|
|
t/RemoteDB/HIV/HIVQuery.t .............. ok
|
|
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
|
|
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
|
|
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
|
|
t/RemoteDB/RefSeq.t .................... ok
|
|
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
|
|
t/RemoteDB/SeqVersion.t ................ ok
|
|
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
|
|
t/RemoteDB/Taxonomy.t .................. ok
|
|
t/Restriction/Analysis-refac.t ......... ok
|
|
t/Restriction/Analysis.t ............... ok
|
|
t/Restriction/Gel.t .................... ok
|
|
t/Restriction/IO.t ..................... ok
|
|
t/Root/Exception.t ..................... ok
|
|
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
|
|
t/Root/IO.t ............................ ok
|
|
t/Root/RootI.t ......................... ok
|
|
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
|
|
t/Root/Storable.t ...................... ok
|
|
t/Root/Utilities.t ..................... ok
|
|
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
|
|
t/SearchIO/CigarString.t ............... ok
|
|
t/SearchIO/SearchIO.t .................. ok
|
|
t/SearchIO/SimilarityPair.t ............ ok
|
|
t/SearchIO/Tiling.t .................... ok
|
|
t/SearchIO/Writer/GbrowseGFF.t ......... ok
|
|
t/SearchIO/Writer/HSPTableWriter.t ..... ok
|
|
t/SearchIO/Writer/HTMLWriter.t ......... ok
|
|
t/SearchIO/Writer/HitTableWriter.t ..... ok
|
|
t/SearchIO/Writer/TextWriter.t ......... ok
|
|
t/SearchIO/axt.t ....................... ok
|
|
t/SearchIO/blast.t ..................... ok
|
|
t/SearchIO/blast_pull.t ................ ok
|
|
t/SearchIO/blasttable.t ................ ok
|
|
t/SearchIO/cross_match.t ............... ok
|
|
t/SearchIO/erpin.t ..................... ok
|
|
t/SearchIO/exonerate.t ................. ok
|
|
t/SearchIO/fasta.t ..................... ok
|
|
t/SearchIO/gmap_f9.t ................... ok
|
|
t/SearchIO/hmmer.t ..................... ok
|
|
t/SearchIO/hmmer_pull.t ................ ok
|
|
t/SearchIO/infernal.t .................. ok
|
|
t/SearchIO/megablast.t ................. ok
|
|
t/SearchIO/psl.t ....................... ok
|
|
t/SearchIO/rnamotif.t .................. ok
|
|
t/SearchIO/sim4.t ...................... ok
|
|
t/SearchIO/waba.t ...................... ok
|
|
t/SearchIO/wise.t ...................... ok
|
|
t/Seq/DBLink.t ......................... ok
|
|
t/Seq/EncodedSeq.t ..................... ok
|
|
t/Seq/LargeLocatableSeq.t .............. ok
|
|
t/Seq/LargePSeq.t ...................... ok
|
|
t/Seq/LocatableSeq.t ................... ok
|
|
t/Seq/MetaSeq.t ........................ ok
|
|
t/Seq/PrimaryQual.t .................... ok
|
|
t/Seq/PrimarySeq.t ..................... ok
|
|
t/Seq/PrimedSeq.t ...................... ok
|
|
t/Seq/Quality.t ........................ ok
|
|
t/Seq/Seq.t ............................ ok
|
|
t/Seq/SimulatedRead.t .................. ok
|
|
t/Seq/WithQuality.t .................... ok
|
|
t/SeqEvolution.t ....................... ok
|
|
t/SeqFeature/Amplicon.t ................ ok
|
|
t/SeqFeature/Clone.t ................... ok
|
|
t/SeqFeature/Collection.t .............. ok
|
|
t/SeqFeature/Computation.t ............. ok
|
|
t/SeqFeature/FeaturePair.t ............. ok
|
|
t/SeqFeature/Gene.t .................... ok
|
|
t/SeqFeature/Generic.t ................. ok
|
|
t/SeqFeature/Location.t ................ ok
|
|
t/SeqFeature/LocationFactory.t ......... ok
|
|
t/SeqFeature/Primer.t .................. ok
|
|
t/SeqFeature/Range.t ................... ok
|
|
t/SeqFeature/RangeI.t .................. ok
|
|
t/SeqFeature/SeqAnalysisParser.t ....... ok
|
|
t/SeqFeature/SubSeq.t .................. ok
|
|
t/SeqFeature/Unflattener.t ............. ok
|
|
t/SeqIO/Handler.t ...................... ok
|
|
t/SeqIO/MultiFile.t .................... ok
|
|
t/SeqIO/Multiple_fasta.t ............... ok
|
|
t/SeqIO/SeqBuilder.t ................... ok
|
|
t/SeqIO/SeqIO.t ........................ ok
|
|
t/SeqIO/Splicedseq.t ................... ok
|
|
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqIO/ace.t .......................... ok
|
|
t/SeqIO/agave.t ........................ ok
|
|
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqIO/asciitree.t .................... ok
|
|
t/SeqIO/bsml.t ......................... ok
|
|
t/SeqIO/bsml_sax.t ..................... ok
|
|
t/SeqIO/chadoxml.t ..................... ok
|
|
t/SeqIO/chaos.t ........................ ok
|
|
t/SeqIO/chaosxml.t ..................... ok
|
|
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqIO/embl.t ......................... ok
|
|
t/SeqIO/entrezgene.t ................... ok
|
|
t/SeqIO/excel.t ........................ ok
|
|
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqIO/fasta.t ........................ ok
|
|
t/SeqIO/fastq.t ........................ ok
|
|
t/SeqIO/flybase_chadoxml.t ............. ok
|
|
t/SeqIO/game.t ......................... ok
|
|
t/SeqIO/gbxml.t ........................ ok
|
|
t/SeqIO/gcg.t .......................... ok
|
|
t/SeqIO/genbank.t ...................... ok
|
|
t/SeqIO/interpro.t ..................... skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
|
|
t/SeqIO/kegg.t ......................... ok
|
|
t/SeqIO/largefasta.t ................... ok
|
|
t/SeqIO/lasergene.t .................... ok
|
|
t/SeqIO/locuslink.t .................... ok
|
|
t/SeqIO/mbsout.t ....................... ok
|
|
t/SeqIO/metafasta.t .................... ok
|
|
t/SeqIO/msout.t ........................ ok
|
|
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
|
|
t/SeqIO/nexml.t ........................ ok
|
|
t/SeqIO/phd.t .......................... ok
|
|
t/SeqIO/pir.t .......................... ok
|
|
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqIO/qual.t ......................... ok
|
|
t/SeqIO/raw.t .......................... ok
|
|
t/SeqIO/scf.t .......................... ok
|
|
t/SeqIO/seqxml.t ....................... ok
|
|
t/SeqIO/strider.t ...................... ok
|
|
t/SeqIO/swiss.t ........................ ok
|
|
t/SeqIO/tab.t .......................... ok
|
|
t/SeqIO/table.t ........................ ok
|
|
t/SeqIO/tigr.t ......................... ok
|
|
t/SeqIO/tigrxml.t ...................... ok
|
|
t/SeqIO/tinyseq.t ...................... ok
|
|
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
|
|
t/SeqTools/Backtranslate.t ............. ok
|
|
t/SeqTools/CodonTable.t ................ ok
|
|
t/SeqTools/ECnumber.t .................. ok
|
|
t/SeqTools/GuessSeqFormat.t ............ ok
|
|
t/SeqTools/OddCodes.t .................. ok
|
|
t/SeqTools/SeqPattern.t ................ ok
|
|
t/SeqTools/SeqStats.t .................. ok
|
|
t/SeqTools/SeqUtils.t .................. ok
|
|
t/SeqTools/SeqWords.t .................. ok
|
|
t/Species.t ............................ ok
|
|
t/Structure/IO.t ....................... ok
|
|
t/Structure/Structure.t ................ ok
|
|
t/Symbol.t ............................. ok
|
|
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
|
|
t/Tools/Alignment/Consed.t ............. ok
|
|
t/Tools/AmpliconSearch.t ............... ok
|
|
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
|
|
t/Tools/Analysis/Protein/Scansite.t .... ok
|
|
t/Tools/Analysis/Protein/Sopma.t ....... skipped: Network tests have not been requested
|
|
t/Tools/EMBOSS/Palindrome.t ............ ok
|
|
t/Tools/Est2Genome.t ................... ok
|
|
t/Tools/FootPrinter.t .................. ok
|
|
t/Tools/GFF.t .......................... ok
|
|
t/Tools/Geneid.t ....................... ok
|
|
t/Tools/Genewise.t ..................... ok
|
|
t/Tools/Genomewise.t ................... ok
|
|
t/Tools/Genpred.t ...................... ok
|
|
t/Tools/Hmmer.t ........................ ok
|
|
t/Tools/IUPAC.t ........................ ok
|
|
t/Tools/Lucy.t ......................... ok
|
|
t/Tools/Match.t ........................ ok
|
|
t/Tools/Phylo/Gerp.t ................... ok
|
|
t/Tools/Phylo/Molphy.t ................. ok
|
|
t/Tools/Phylo/PAML.t ................... ok
|
|
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
|
|
t/Tools/Primer3.t ...................... ok
|
|
t/Tools/Promoterwise.t ................. ok
|
|
t/Tools/Pseudowise.t ................... ok
|
|
t/Tools/QRNA.t ......................... ok
|
|
t/Tools/RandDistFunctions.t ............ ok
|
|
t/Tools/RepeatMasker.t ................. ok
|
|
t/Tools/Run/RemoteBlast.t .............. skipped: Network tests have not been requested
|
|
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
|
|
t/Tools/Seg.t .......................... ok
|
|
t/Tools/SiRNA.t ........................ ok
|
|
t/Tools/Sigcleave.t .................... ok
|
|
t/Tools/Signalp.t ...................... ok
|
|
t/Tools/Signalp/ExtendedSignalp.t ...... ok
|
|
t/Tools/Sim4.t ......................... ok
|
|
t/Tools/Spidey/Spidey.t ................ ok
|
|
t/Tools/TandemRepeatsFinder.t .......... ok
|
|
t/Tools/TargetP.t ...................... ok
|
|
t/Tools/Tmhmm.t ........................ ok
|
|
t/Tools/ePCR.t ......................... ok
|
|
t/Tools/pICalculator.t ................. ok
|
|
t/Tools/tRNAscanSE.t ................... ok
|
|
t/Tree/Compatible.t .................... ok
|
|
t/Tree/Node.t .......................... ok
|
|
t/Tree/PhyloNetwork/Factory.t .......... ok
|
|
t/Tree/PhyloNetwork/GraphViz.t ......... ok
|
|
t/Tree/PhyloNetwork/MuVector.t ......... ok
|
|
t/Tree/PhyloNetwork/PhyloNetwork.t ..... ok
|
|
t/Tree/PhyloNetwork/RandomFactory.t .... ok
|
|
t/Tree/PhyloNetwork/TreeFactory.t ...... ok
|
|
t/Tree/RandomTreeFactory.t ............. ok
|
|
t/Tree/Tree.t .......................... ok
|
|
t/Tree/TreeIO.t ........................ ok
|
|
t/Tree/TreeIO/lintree.t ................ ok
|
|
t/Tree/TreeIO/newick.t ................. ok
|
|
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
|
|
# Begin tests for writing tree files
|
|
t/Tree/TreeIO/nexml.t .................. ok
|
|
t/Tree/TreeIO/nexus.t .................. ok
|
|
t/Tree/TreeIO/nhx.t .................... ok
|
|
t/Tree/TreeIO/phyloxml.t ............... ok
|
|
t/Tree/TreeIO/svggraph.t ............... ok
|
|
t/Tree/TreeIO/tabtree.t ................ ok
|
|
t/Tree/TreeStatistics.t ................ ok
|
|
t/Variation/AAChange.t ................. ok
|
|
t/Variation/AAReverseMutate.t .......... ok
|
|
t/Variation/Allele.t ................... ok
|
|
t/Variation/DNAMutation.t .............. ok
|
|
t/Variation/RNAChange.t ................ ok
|
|
t/Variation/SNP.t ...................... ok
|
|
t/Variation/SeqDiff.t .................. ok
|
|
t/Variation/Variation_IO.t ............. ok
|
|
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
|
|
t/nexml.t .............................. ok
|
|
All tests successful.
|
|
|
|
Test Summary Report
|
|
-------------------
|
|
t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0)
|
|
TODO passed: 109, 112, 115, 118
|
|
Files=325, Tests=23238, 74 wallclock secs ( 3.50 usr 1.48 sys + 67.67 cusr 4.25 csys = 76.90 CPU)
|
|
Result: PASS
|
|
Building BioPerl
|
|
Reading skip patterns from 'INSTALL.SKIP'.
|
|
Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/man/man1/bp_mutate.pl.1 (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_nexus2nh.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_pairwise_kaks.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqret.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_parse_hmmsearch.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_classify_hits_kingdom.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seq_length.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_taxonomy2tree.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_blast2tree.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_hivq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_dbsplit.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_filter_search.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_fetch.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_revtrans-motif.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_das_server.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqretsplit.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_mutate.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_download_query_genbank.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqfeature_delete.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_composite_LD.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_extract_feature_seq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_mrtrans.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_sreformat.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqcut.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_process_sgd.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqfeature_load.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_translate_seq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_generate_histogram.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqfeature_gff3.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_search2gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_oligo_count.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_bulk_load_gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_unflatten_seq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_heterogeneity_test.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_search2alnblocks.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_tree2pag.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_fast_load_gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_gccalc.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_split_seq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_biofetch_genbank_proxy.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_process_wormbase.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_biogetseq.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_genbank2gff3.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_nrdb.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_search2table.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_index.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqpart.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_genbank2gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_aacomp.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_fastam9_to_table.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_local_taxonomydb_query.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_query_entrez_taxa.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_chaos_plot.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_process_gadfly.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_mask_by_search.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_find-blast-matches.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_meta_gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_search2tribe.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_make_mrna_protein.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_load_gff.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_flanks.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_remote_blast.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_seqconvert.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_taxid4species.pl (unchanged)
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Skipping /home/ryan/perl5/perlbrew/perls/perl-blead/bin/bp_bioflat_index.pl (unchanged)
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Writing /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux/auto/Bio/.packlist
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|
OK
|
|
Successfully installed BioPerl-1.007001
|
|
Installing /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux/.meta/BioPerl-1.007001/install.json
|
|
! Installing the dependencies failed: Missing version info for module 'Bio::Root::Root'
|
|
! Bailing out the installation for Bio-GeneDesign-5.54.
|
|
! Installing the dependencies failed: Module 'Bio::Tools::Run::StandAloneBlastPlus' is not installed, Module 'Bio::GeneDesign::Basic' is not installed, Module 'Time::Format' is not installed
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|
! Bailing out the installation for Bio-BioStudio-1.05.
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|
1 distribution installed
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|
Command [cpanm --reinstall --verbose Bio::BioStudio::Basic] terminated with exit code 1 ($? = 256) under the following perl environment:
|
|
Command terminated with non-zero status.
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Current perl:
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Name: perl-blead
|
|
Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
|
|
Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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Compiled at: Mar 30 2017 03:10:09
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perlbrew:
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|
version: 0.78
|
|
ENV:
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|
PERLBREW_ROOT: /home/ryan/perl5/perlbrew
|
|
PERLBREW_HOME: /home/ryan/.perlbrew
|
|
PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
|
|
PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
|