Run 1.2.2 1.4.0 delta

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

Removed all references to submitting bugs 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::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/.