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; Bug #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 Bug #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: Bug #1507, SYNOPSIS is runnable now with API changes; Bug #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; Bug #1928; Bug #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: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::codonw: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::comalign: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::combat: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::compseq: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::con_filter: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::confmat: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::cons: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::consense: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::consensus: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::cpgplot: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::cpgreport: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::cusp: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::cutseq: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::dan: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::dca: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

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: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::descseq: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::dialign2: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::diffseq: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::digest: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::distmat: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::distquart: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::dnadist: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::dnapars: Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

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