Run 1.2.2 1.4.0 delta

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These are detailed notes on changes made between bioperl-run-release-1-2-2 and bioperl-run-devel-1-4-0.

Bio::Factory::EMBOSS
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Emboss version number parsing -- could have sworn I already checked this in per-1.5.1, apparently not
Prog, not factory
Bio::Installer::Clustalw
Adding class
Bio::Installer::EMBOSS
Added
Changing from hardcoded version to EMBOSS-latest
EMBOSS-latest version bug
Added FIXME
Less spam - more ham
Bio::Installer::Generic
Added
Less spam - more ham
Bio::Installer::Muscle
First version
Bio::Installer::PAML
Added
Updating to 3.14a version
Updating directory_name to version 3.14
Less spam - more ham
Updated to 3.15 and http dir
Bio::Installer::Probcons
Adding a probcons installer - watch out for newer releases than 'PACKAGE_NAME' => 'probcons_v1_09.tar.gz'
Less spam - more ham
Bio::Installer::TCoffee
Added
Less spam - more ham
Updated to 4.45
Bio::Tools::Run::AbstractRunner
Proposed fundamental classes for other specific classes
Bio::Tools::Run::Alignment::Amap
Copy/pasted from probcons -- see FIXMEs
Fixing version method
Adding switches and params
Adding amap options -- not extensively checked though
Let Bio::Tools::Run::WrapperBase handle error_string
Bio::Tools::Run::Alignment::Blat
Well, at least it runs the blat program now, although it isn't seemingly able to find the output tempfile to retrieve the results
Various fixes to get blat runnable in line with bioperl-live 1.2.3 all tests now pass.
This still needs an overhaul but fix minor doc bugs in naming the module
Stan's fix
Executable is the string to run
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::Clustalw
Nathan's version of the module
More, better tests for the new implementation for tree/bootstrap -- still some things to fix
Issue #1646; This should go with msf if gcg format is requested
Some Documentation fixes to clarify how to set the env variables so that it shows up in the perldoc not just as comments
Adhere to the style that makes sense to me
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::DBA
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::Exonerate
Wrapper for exonerate
Doc fix
Properly run Exonerate
Bio::Tools::Run::Alignment::Kalign
Adding Kalign.pm from a copy/paste of Muscle.pm -- havent tested all the options and switches yet
Bio::Tools::Run::Alignment::Lagan
Allowing of setting of outfile
Can't declare are expect a variable at the same time
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Expected envvariable changed to LAGAN_DIR to match that used by lagan itself, work-around for sort sytax bug in lagan script
LAGAN_DIR is now required, files are cleaned up
Bio::Tools::Run::Alignment::MAFFT
More, better tests for the new implementation for tree/bootstrap -- still some things to fix
Update link
Tcoffee --> MAFFT, version stuff removed, allow percent ID to waver a little
Fixed parsing of version number while keeping backward compatibility
Use rel2abs from File::Spec not Bio::Root::IO. Also, compily with some Bioperl best practices
Bio::Tools::Run::Alignment::Muscle
Bare Bones MUSCLE wrapper and tests
Adding params to be able to run refine option
Added maxiters and tree1 options
Test more muscle args, fix new {} _rearrage with mixed args
Support for the soon-to-be-released update cmdline option '-scorefile'
Added GAPOPEN option -- havent tested at all
Adding KBAND in MUSCLE_PARAMS -- beware that this option only works for the discontinued version 6 of muscle
Recommend usage of v3.6, tests only run with >= 3.6
Adding profile option -- does not work for 3.6 but 3.52 -- please shout if you see something wrong
V3.6 profile comment
Bio::Tools::Run::Alignment::Probalign
First version of the probalign wrapper -- modified from Probcons.pm
Bio::Tools::Run::Alignment::Probcons
Probcons wrapper -- first try!!!
Adding params and switches
Uppercase params and switches
FIXME: last line switches - dunno how to set them
Fixing double dashes and equal signs
Probcons is a bit inconsistent with this flag
Some modes of operation do no generate an output alignment
Bio::Tools::Run::Alignment::Sim4
Michael's patch
Allow alignment methods (A=[01234]) to be specified, default to A=0 as before
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::StandAloneFasta
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::TCoffee
Adding null matrix capability and score_ascii
small docu fixes
Some Documentation fixes to clarify how to set the env variables so that it shows up in the perldoc not just as comments
Albert's patch
Small cosmetic changes
Profile align expects 1st arg to be profile, second to be seq
Adhere to the style that makes sense to me
Profile-related bug fixed, general issue with special characters causing failure or warnings solved
-no_warning only works and is only needed on certain versions of TCoffee
Bio::Tools::Run::Analysis
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Analysis::soap
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory::Pise
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory::soap
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Cap3
Add Marc's module
Bio::Tools::Run::Coil
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Some clarification of COILSDIR
Bio::Tools::Run::EMBOSSApplication
No need for this debugging
Allow 0 value attributes per Susan Miller's bug report
Debugging enabled
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Add executable(), program_dir(), program_path()
Write executable() method, t/EMBOSS.t tests pass now
Bio::Tools::Run::EMBOSSacd
Stephen's patch
EMBOSS 3.0.0 testing passes
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Eponine
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Now correct usage for EPONINEDIR if it is a dir or pointing at the actual jar file
Bio::Tools::Run::FootPrinter
Fix stupidity with tempfilehandle and outfh not being closed properly as reported by Ben Westover
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
FOOTPRINTER_DIR env var is required
Bio::Tools::Run::Genewise
Docfix, an array of genes can be returned
Genewise tests should pass now on 2.2.3 and 2.2.0
Test for wise 2.2.0 and 2.2.3
Bio::Tools::Run::Genscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Hmmer
Hmmer wrapper factory, currently supports hmmsearch, hmmalign,hmmpfam, hmmbuild and hmmcalibrate
Fixes option to allow -n and also allow -arguments
Cleanup code for debugging
Fix filehandle problem without using IO::String -- problem before was FH was getting closed because it went out of scope
Scott Markel's additions + some tweaking for hmmalign; Added many more cmd-line options plus support for doubledash arguments and force -q option on hmmalign
Switch flag per Issue #1775
Bio::Tools::Run::Hmmpfam
Hmmpfam deprecated, replacted by Hmmer
Bio::Tools::Run::JavaRunner
Proposed fundamental classes for other specific classes
Bio::Tools::Run::Mdust
Use save_tempfiles, use PROGRAMNAME as a variable, use tempfile instead of randomly generating filename
Modified call to io->tmpfile to get file name as well as handle
Bio::Tools::Run::Phrap
Phrap wrapper
Teeny code cleanup
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Forester::SDI
SDI in Forester package. it should be announced that you need to modify the source code of SDI to stop the popup window, if you only need the output file of it, before using this module
More document
Bio::Tools::Run::Phylo::LVB
Adding Daniel's LVB wrapper
LVB changes by Daniel
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Molphy::ProtML
Align the code
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::PAML::Baseml
Add Baseml
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Codeml -> baseml, but still doesn't quite work, baseml is VERY picky about sequence file input format and I can't figure out what is being written wrong. I moved to using wrapped sequential rather than whole line, I tried moving ids to their own line, and I tried with or without lots of padding at end of id string. Very frustrating....
Bio::Tools::Run::Phylo::PAML::Codeml
Default should be an arrayref
George Hartzell fixes
What is that underscore in there for?
Stupid jason - it saves a syscall
Docu fix
Let alpha be more free - don't try and restrict it
Support more models
Allow alignment to be specified in run()
Some docu update
Update doc
Allow omega to varied
Adding allowed fix_blength = 1
Added no_param_checks getter-setter -- added no_param_checks condition in set_parameter
Silence undef warning
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
This prepare function is very similar to run -- should split run in the future
Allow output filename to be specified
Email addr mangle; don't double write outfile, quiet when not defined
Bio::Tools::Run::Phylo::PAML::Evolver
WARNING - only a skeleton - C-s FIXME in emacs
Start some fleshing in prepare method -- some FIXMEs need consideration
Back from the bus -- still not functional at all
Prepare method needs codonfreqs stuff and some newick love
Some more clear FIXME tags
It will prepare the stuff with codonfreqs now -- problem with trees -- still a lot of FIXMEs to solve
No internal ids in the tree - this needs nointernalids.patch in newick.pm
Adding rootseq fixme
Some more comments
This is still very rudimentary -- wear you seatbelt at all times
Adding alignment method and indel getset -- a bit of cleaning
Bio::Tools::Run::Phylo::PAML::Yn00
Issue #1507, SYNOPSIS is runnable now with API changes
Issue #1507 add MSwin .exe extension where appropriate
Wait -this isn't necessary , we already pad the PROGRAMNAME with the .exe when appropriate
George Hartzell fixes
Catfile not catdir
Allow alignment to be passed in to run()
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Email addr mangle; don't double write outfile, quiet when not defined
Bio::Tools::Run::Phylo::Phylip::Base
Protdist works for me on phylip 3.61
DrawTree Basically works
Bio::Tools::Run::Phylo::Phylip::Consense
No more "Using a hash as a reference is deprecated" warnings
Do the right thing that I wanted you to do (you know that thing)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::DrawGram
Drawgram works
DrawTree Basically works
Bio::Tools::Run::Phylo::Phylip::DrawTree
DrawTree Basically works
Issue #1928
Issue #2040
Bio::Tools::Run::Phylo::Phylip::Neighbor
Properly get the hash value
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::PhylipConf
Bug fix, shouldn't writing Y to change MODEL type
No more "Using a hash as a reference is deprecated" warnings
Protdist works for me on phylip 3.61
Indent some code
Drawgram works
DrawTree Basically works
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::ProtDist
Get rid of deprecation warning
Protdist works for me on phylip 3.61
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::ProtPars
No more "Using a hash as a reference is deprecated" warnings
Do the right thing that I wanted you to do (you know that thing)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::SeqBoot
No more "Using a hash as a reference is deprecated" warnings
Support new exported Menu variable
Bio::Tools::Run::PiseApplication
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::Puzzle
Phyml is a program for estimating large phylogenies by maximum likelihood. New version of Puzzle (5.2).
Bio::Tools::Run::PiseApplication::abiview
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::addquart
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::align2model
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::alistat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::antigenic
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::assp
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::backtranseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bambe
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::banana
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bionj
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::biosed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bl2seq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blast2
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps_block
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps_matrix
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::boxshade
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::btwisted
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cai
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cap
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cds
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::chaos
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::charge
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::checktrans
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::chips
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cirdna
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clique
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clustalw
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clustalw_convert
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codcmp
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::coderet
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codnocod
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codontree
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Bio::Tools::Run::PiseApplication::codonw
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Bio::Tools::Run::PiseApplication::comalign
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Bio::Tools::Run::PiseApplication::combat
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Bio::Tools::Run::PiseApplication::compseq
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Bio::Tools::Run::PiseApplication::con_filter
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Bio::Tools::Run::PiseApplication::confmat
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Bio::Tools::Run::PiseApplication::cons
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Bio::Tools::Run::PiseApplication::consense
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Bio::Tools::Run::PiseApplication::consensus
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Bio::Tools::Run::PiseApplication::cpgplot
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Bio::Tools::Run::PiseApplication::cpgreport
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Bio::Tools::Run::PiseApplication::cusp
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Bio::Tools::Run::PiseApplication::cutseq
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Bio::Tools::Run::PiseApplication::dan
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Bio::Tools::Run::PiseApplication::dca
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Bio::Tools::Run::PiseApplication::decorate
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Bio::Tools::Run::PiseApplication::degapseq
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Bio::Tools::Run::PiseApplication::descseq
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Bio::Tools::Run::PiseApplication::dialign2
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Bio::Tools::Run::PiseApplication::diffseq
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Bio::Tools::Run::PiseApplication::digest
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Bio::Tools::Run::PiseApplication::distmat
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Bio::Tools::Run::PiseApplication::distquart
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Bio::Tools::Run::PiseApplication::dnadist
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Bio::Tools::Run::PiseApplication::dnapars
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Bio::Tools::Run::PiseApplication::dollop
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::domainer
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dotmatcher
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dotpath
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dottup
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawgram
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawpyr
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawtree
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dreg
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::druid
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dsc
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dssp
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::einverted
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::emma
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::emowse
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::environ
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::eprimer3
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::equicktandem
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::est2genome
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::etandem
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::extractfeat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::extractseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fasta
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fastdnaml
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fastrna
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::filtersites
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::findkm
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fitch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fmtseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::freak
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzznuc
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzzpro
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzztran
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gb2xml
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::geecee
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::genscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::getblock
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::getorf
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gff2ps
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gibbs
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gibbs_scan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::golden
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::grailclnt
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gruppi
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::helixturnhelix
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmbuild
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmcalibrate
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmconvert
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmemit
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmer2sam
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmfetch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmpfam
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmscore
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmsearch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmoment
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::homology
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::html4blast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::iep
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::infoalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::infoseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::interface
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::isochore
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::kitsch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lassap
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lgicsearch
Removing application LGICSEARCH upon request of the author
Bio::Tools::Run::PiseApplication::lindna
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::listor
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::loadseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lvb
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::makehist
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::map
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::marscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::maskfeat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::maskseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::matcher
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::megamerger
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::melting
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::merger
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mfold
Pise/bioperl module for a recent version of mfold (3.1.2).
Mfold version change (3.1.2)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mix
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::modelfromalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mreps
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::msa
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::msbar
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mspcrunch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mview_alig
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mview_blast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mwfilter
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::needle
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::neighbor
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newcpgreport
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newcpgseek
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::njdist
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nnssp
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::notseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nrscope
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nthseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::octanol
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::oddcomp
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::palindrome
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pam
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::parciquart
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pars
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pasteseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patmatdb
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patmatmotifs
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patser
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pdbsearch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepcoil
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepinfo
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepnet
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepstats
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwheel
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwindow
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwindowall
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pestfind
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pftools
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::phiblast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::phyml
Phyml is a program for estimating large phylogenies by maximum likelihood. New version of Puzzle (5.2).
Bio::Tools::Run::PiseApplication::pima
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plotcon
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plotorf
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plsearch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::polydot
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pratt
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::predator
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::preg
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyplot
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::primersearch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::primo
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prodom
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::profit
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prophecy
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prophet
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prose
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prot_nucml
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protal2dna
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protdist
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protpars
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::psiblast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::psort2
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pyramids
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pyreval
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::qstar
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::quicktree
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::readnexus
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::readseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::recoder
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::redata
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::remap
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::repeats
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::restover
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::restrict
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::revseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnadistance
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaeval
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnafold
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaga
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaheat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnainverse
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnapdist
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnasubopt
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sam2hmmer
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sampleseqs
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::saps
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::satellites
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scan_for_matches
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scope
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scopparse
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqboot
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqgen
Changes in parameters: - added options invar_site (-i), random_seed (-z), write-ancest (-wa), write-sites (-wr), partition_numb (-p) - fixed bug in Phylip option: it was -p now it's a vlist: -op, -or, -on - changed type of some options type from integer to float (scale_branch, scale_tree, rate123, shape, freqACGT, transratio)
- pb in some variable names: changed '-' to '_'
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqmatchall
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqsblast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqstat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showfeat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showorf
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::shuffleseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sigcleave
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::siggen
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sigscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::silent
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sirna
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::splitter
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sreformat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stretcher
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stride
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stssearch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::supermatcher
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::syco
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tacg
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tfscan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tipdate
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tmap
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::toppred
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tranalign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::transeq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::treealign
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trimest
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trimseq
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trnascan
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::twofeat
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::unroot
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::vectorstrip
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::water
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::weighbor
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::whichdb
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wise2
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wobble
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wordcount
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wordmatch
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wublast2
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::xblast
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::xpound
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseJob
Sub fh(): the test to compare the requested file and the url in the list of results was not appropriate.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Added CLOSE() tied filehandle method (Issue #2126) to properly close tied filehandle. Still has redef'd sub warnings.
Bio::Tools::Run::PiseJobParser
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseWorkflow
PiseWorkflow is a module for building and running a workflow on top of PiseApplication instances.
Bio::Tools::Run::Primate
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Primer3
Porting Rob Edwards extension of Primer3 wrapper and parser
Changed Bio::Tools::Run::Primer3 to allow get/set of program name and directory
Attempted cleanup of code for Issue #1657
Patch applied
Some code formatting
Let's put the new new() example up top so no one misses it
6th inning, 6th game, Sox up by 4! Can't do much else but hit the tab key.
Minor change to program_dir in Bio::Tools::Run::Primer3 which could never be set and then checked later
Minor change to included_region in Bio::Tools::Run::Primer3 to make default set correctly
George Hartzell's excellent code fixes
Let's try this
Mention release 1 compatibility
_set_variable() was in Bio/Tools/Primer3.pm but was unused by that module, actually used only by Bio/Tools/Run/Primer3.pm so move it there
I was wrong, better testing shows that _set_variable is better kept here
Small code/doc cleanup
Bio::Tools::Run::Prints
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Profile
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Pseudowise
An hour of my life gone... pseudowise wrapper is now better suited to actually work and separate parsing from running
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::RepeatMasker
Operate happily with new open-version
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Seg
Initial commit
Previous commit on this module by mistaken. reverted in this commit
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Signalp
Fixed truncation bug
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Tmhmm
Tcoffee --> MAFFT, version stuff removed, allow percent ID to waver a little
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
TMHMMDIR is required
Enabled TMHMMDIR envvar requirment
Remove directory generated by tmhmm during run
Fixed to set -basedir properly and to use tempdir for working directory
Bio::Tools::Run::TribeMCL
Jump out of parser loop when we hit the stats at the bottom of the report (I think this did not used to be there)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Sane Species creation
Bio::Tools::Run::Vista
Added java param to allow setting of java parameters, for example to set higher heap sizes..
Major bug, need to project aligmnents, basically need to remove position in pairwise aligmnet if both are gap characters, else vista will count wrongly
Allow more than one references to be selected
Fix from Jonathan Manning
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Update some errors in doc
Build.PL
New Build.PL install system, Makefile.PL still works but warns
Makefile.PL
George Hartzell fixes
Version updates
Now using %packages for WriteMakefile
Check Bioperl is installed before proceeding with makefile
Better test for existing Bioperl installation
New-style with added features and implementation of the pise email question
Removed unneccessary use, corrected email question
Clearer version checking
Good style for ¬$VERSION
Do not die, just warn when required things are missing
Some modules don't define VERSION, default to 0
New Build.PL install system, Makefile.PL still works but warns
ModuleBuildBioperl.pm
New Build.PL install system, Makefile.PL still works but warns
Update fix from core
scripts/bioperl_application_installer.PLS
Changed name of file installer.PLS to bioperl_application_installer.PLS
Less spam - more ham
scripts/installer.PLS
Adding installer.PLS
Changed name of file installer.PLS to bioperl_application_installer.PLS
scripts/multi_hmmsearch.PLS
Add Mauricio's script
scripts/panalysis.PLS
Patched, thank you Albert
Revision string fix
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
scripts/papplmaker.PLS
Revision string fix
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
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