Run 1.4.0 1.5.1 delta

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These are detailed notes on changes made between bioperl-run-devel-1-4-0 and bioperl-run-release-1-5-1.

Bio::Factory::EMBOSS: Moving from bioperl-live CVS module; Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

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::PAML: Added; Updating to 3.14a version; Updating directory_name to version 3.14; Less spam - more ham

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

Bio::Tools::Run::AbstractRunner: Proposed fundamental classes for other specific classes

Bio::Tools::Run::Alignment::Blat: Moving to Bio::Tools::Run::Alignment Namespace; Some code cleanup to avoid warnings and insure filehandles are properly closed, etc; 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: Migrated code that runs tools to Bio::Tools::Run; Renaming packages for new dir structure; Fixed to PROPER usage of tempfile; More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files; Quoted unquoted string literals used as hash keys.; Migrated to new Bio::Root::RootI chained new; Changed to adopt Bio::Root::IO.; Properly removing tempfiles; Io was not initialized, meaning tempfiles were not cleaned up; Intitialize io -- facilitate tempfile cleanup; The module was requiring input sequences to eq Bio::Seq, changed that to isa->Bio::PrimarySeqI. Clustalw chrashes if the the sequence does not have id() set, undef id() now throws an error.; Checks that seq is a Bio::PrimarySeq and seq->id() is set; Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.; The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.; The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.; Changed exists_clustal() to use new Bio::Root::IO->exists_exe().; Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.; More quiet warning so tests are less chatty; Check to insure defined object before calling ISA; Use the updated PROGRAM exe location information to set the PROGRAM variable; Added method version() $self->isa('Bio::Factory::ApplicationFactoryI'); Debug message now uses the debug method; Verbosity=-1 is same as quiet(); Params should be appended not overwriting; No need for the dir variable; Now can take a program path as arg on the new method, aboids need for ENV variable (ENV still in not to break other people's scripts,etc); Tweak to clustalw test for falling over correctly; Turn of clustalw debugging; Slightly more intelligent checking for clustalw exe; Merged exe checking from branch; Minor documentation fixes; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Allow phylip output format to be set; Make sure we cleanup tempfiles before each run; Make sure we've closed temporary file handles; Some changes to deal with dec_osf bug; Moving executable method to Wrapper base, removing global TMP variables where possible; Closing AlignIO to avoid too many open files error; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: Wrapper object for Ewan Birney's Dna Block Aligner; Changed to use PAML template for find executable insated of ClustalW way; Fixed tempdir, inherit from wrapperbase; Doh left out tempdir bug; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; To Quieten declaration warnings; Removed all references to submitting bugs 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::Lagan: Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Swapping order so that it won't fail on an isa of an array; Small fixes and addition of options; Really should include the program name; Added the right credits.; 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/.

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

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'

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

Bio::Tools::Run::Alignment::Sim4: Sim4 wrapper; Housekeeping for open files; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; To Quieten declaration warnings; 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: Committing first port of StandAloneFasta from Tiequan, may not be fully functional; Fix bug; Argh left out program_dir; Small fixes for linux and setting of program param correctly; Need to override executable to store multiple program namesTempfile cleanup may not be correct - need to verify; Support -S and a place to put the 'output' data - although not used yet; Bug which was not caught before; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Removed all references to submitting bugs 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: Migrated code that runs tools to Bio::Tools::Run; Renaming packages for new dir structure; Fixed to PROPER usage of tempfile; Extra documentation; More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files; Quoted unquoted string literals used as hash keys.; Migrated to new Bio::Root::RootI chained new; Fixed several doc format bugs.; Correct authors + email for consistency; Changed to adopt Bio::Root::IO.; Fixed TCoffee changes to properly output seqs to temp file when passing in array of seqs; Io was not initialized, meaning tempfiles were not cleaned up; Intitialize io -- facilitate tempfile cleanup; Checks that seq is a Bio::PrimarySeq and seq->id() is set; Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.; The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.; The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.; Changed exists_tcoffee() to use new Bio::Root::IO->exists_exe().; Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.; StandAloneBlast now checks for ecoli.nt (is this right?) and TCoffee is a little more verbose; Use the updated PROGRAM exe location information to set the PROGRAM variable; Added version() Implementaion might print an annoying string "FATAL error..." on non-UNIX platforms. Post 1.37 versions of t_coffee will have an explicit -version argument.; Verbosity=-1 is same as quiet(); Version determining regexp protected; Use proper Tools::WrapperBase now; Codeml --> tcoffee copy+paste silliness; More robust parameter handling, matrix is not a required parameter (default of blosum), generic run method now; Make sure we've closed temporary file handles; Moving executable method to Wrapper base, removing global TMP variables where possible; Cleaned docs for cleanup(); Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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

Bio::Tools::Run::Analysis: Added a general Analysis client together with its incarnation as a SOAP client; Added -timeout parameter to the SOAP-based Analysis client; Binary input added; Removed module specific $VERSION, all modules now use global one from Bio::Root::Version; 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: Added a general Analysis client together with its incarnation as a SOAP client; Added -timeout parameter to the SOAP-based Analysis client; Changes in Soaplab API; Changes in Soaplab API; Binary input added; Removed module specific $VERSION, all modules now use global one from Bio::Root::Version; 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: Added a general Analysis client together with its incarnation as a SOAP client; Added -timeout parameter to the SOAP-based Analysis client; Removed module specific $VERSION, all modules now use global one from Bio::Root::Version; 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: Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Email not mandatory anymore in Pise; Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.; - Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-); Removed all references to submitting bugs 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: Added a general Analysis client together with its incarnation as a SOAP client; Changes in Soaplab API; Removed module specific $VERSION, all modules now use global one from Bio::Root::Version; 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::Blat: Wrapper for blat...still under dev; Wrapper for Blat; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Changes in align subroutine taking only one argument; Moving to Bio::Tools::Run::Alignment Namespace

Bio::Tools::Run::Coil: Wrapper for coil; Added quiet param, moving executable method to base class; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::EMBOSSApplication: Classes for wrapping EMBOSS suite; Claning. Needs code to compare input and ACD options; EMBOSS more runnable and w/ tests; Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.; Handle cmd line arguments pointing to a Bio::PrimarySeqI object or array or Bio::PrimarySeqI; Added ability to dump alignments as well as sequences when running an EMBOSS application; Cleanup before each run of an application; Merged changes from trunk to branch; Handle some weird boundary cases; Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero; Explicitly closing some filehandles appears to do a better job freeing resources; No more warnings under perl 5.8.0; Added a missing semicolon to make the synopsis runnable; Use debug to print out the dumper info; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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/.

Bio::Tools::Run::EMBOSSacd: Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero; No more warnings under perl 5.8.0; 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: wrapper for Eponine.. fixed bug; Inherit from WrapperBase; Cleanup of tempfiles works; Fixed Eponine test and runnable; Trying to add sanity to bioperl-run, added checks and pretty failures in the tests... will get there one day; Make sure resources are freed; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; More standardized way of running 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/.

Bio::Tools::Run::FootPrinter: First wrapper for Blanchette's FootPrinter for Phylogenetic Footprinting Todo, take in Bio::Tree for tree_of_life Smarter handling of seq ids; Close file handles; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Cleaned docs for cleanup(); Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Write the files properly; Mark Wagner's enhancements Issue #1399; 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/.

Bio::Tools::Run::Genewise: First addition of Genewise wrapper module; Few small fixes to Genewise runnable and test; Uses the parser in Bio::Tools::Genscan instead of internal parsing; Refactor wrapper; Added -trev option; Remove Fugu system stuff and insure that File tmp handles are closed -- this is what creates the problems of running out of filehandles; Make sure resources are freed; Support -u and -v settings, support passing in file instead of Bio::Seq object (trust user to do the right thing here and passing fastafile; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Support HMMER filetype parameter; Oops - meant to set the HMMER param in the right place, also support another set of GENEWISE parameters; Let's create one less temporary file -- also - let's use the filehandle that was created for us, one less open call, support quiet operation; Quiet properly; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Clarified HMM support. Added checks & exception. Added docs; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Added more options; 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: Wrapper for Genscan executable; POX fixes; Fixing wrapper to be in line with ProtML + WrapperBase; Dumb print statement cuzing failed test; Allow suppression of stderr; Make sure resources are freed; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Doc fix; Removed all references to submitting bugs 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: Wrapper module for hmmpfam; Check for options; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Updated to set params properly and return searchio object; Hmmpfam deprecated, replacted by Hmmer

Bio::Tools::Run::JavaRunner: Proposed fundamental classes for other specific classes

Bio::Tools::Run::Lagan: Moved from bioperl-live. Note: name change: Bio::Tools::Lagan -> Bio::Tools::Run::Lagan; Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace

Bio::Tools::Run::Mdust: Moved Mdust.pm from Bio::Tools to Bio::Tools::Run, added test script and data file.; Some minor changes. Also, I think 'use warnings' has been removed for back-compatibility; Modified documentation to conform to bioperl format; Modified to inherit Bio::Tools::Run::WrapperBase, use Bio::Root::IO to build up paths; 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: Added ProtML wrapper - part of Molphy packager for ML tree building; Codeml->protml doc fixes; Code formatting; Cleanup of tempfiles works; Synopsis doc; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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/.

Bio::Tools::Run::Phylo::PAML::Codeml: PAML package -- codeml wrapper and test committed; Small doc tweaks and added runnable synopsis; POX fixes; Little fixes: catdir -> catfile, better error matching regexp; Migrate from PAMLBase to WrapperBase; Fix internal parameter name; Copy+paste error; Added additions of .exe for on windows, allow alignment to be specified as a file as well as Bio::Align::AlignI object; API changed a little bit with new parser; Cleanup of tempfiles works; Whoops,one more time, cleanup tempfiles and dirs; Cosmetic code fix; Handle exe apps; Default should be F3X4; Respect the original cwd; Refer to the correct base class; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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/.

Bio::Tools::Run::Phylo::PAML::PAMLBase: PAML package -- codeml wrapper and test committed; Migrate from PAMLBase to WrapperBase

Bio::Tools::Run::Phylo::PAML::Yn00: Yn00 wrapper for PAML; Return the values as hash of hashes as they are all pairwise calculations - nei and yang results are returned as 2 separate arrays- this is all going to be improved when we abstract the parsing to a separate parser class; POX fixes; Remove debug copyfile; Migrate from PAMLBase to WrapperBase; Handle windows exes; Fixed to work with new base object and use bioperl PAML parser; Add some debugging support; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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/.

Bio::Tools::Run::Phylo::Phylip::Base: Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps; Tree drawing modules; Use tempdir to run things; First stab at configuration files for managing version difference of phylip; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Protdist works for me on phylip 3.61; DrawTree Basically works

Bio::Tools::Run::Phylo::Phylip::Consense: Wrapper for consense; Allow outgroups to be set using names; Changes to allow multiple alignments, matrices; Moving executable method to Wrapper base, removing global TMP variables where possible; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: Tree drawing modules; Use tempdir to run things; Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming to run method; Don't need to cat tempdir if its an absolute path; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Drawgram works; DrawTree Basically works

Bio::Tools::Run::Phylo::Phylip::DrawTree: Tree drawing modules; Use tempdir to run things; Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming to run method; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; DrawTree Basically works

Bio::Tools::Run::Phylo::Phylip::Neighbor: Added Neighbor-Joining wrapper; Fix warnings; Update some of the docs; Move towards wrapperbase type wrappers; Skip if ret val is 0; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps; Tree drawing modules; Use tempdir to run things; Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly; First stab at configuration files for managing version difference of phylip; Allow outgroups to be set using names; Changes to allow multiple alignments, matrices; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming to run method; Require jumble parameter to be odd or we get ina bad infinite loop; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Check for multiple data sets and set parameter accordingly. Caught by Vladimir.; 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: First stab at configuration files for managing version difference of phylip; Added seqboot; Added consense; Changes to allow multiple alignments, matrices; JIT should be JTT; 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: Wrapper for phylip program protdist which calculates a distance matrix based on amino acid substitution; Removed superfluous variables; Update some of the docs; Doc fix; Brought in line with WrapperBase; Move towards wrapperbase type wrappers; Doh left out tempdir bug; Consistency; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Small formatting changes; Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps; Tree drawing modules; Use tempdir to run things; Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly; First stab at configuration files for managing version difference of phylip; Changes to allow multiple alignments, matrices; Moving executable method to Wrapper base, removing global TMP variables where possible; Formatting; Renaming to run method; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: New wrapper for the phylip program protpars for creating of phylogenetic trees from a multiple alignment; Removed superfluous variables; Move towards wrapperbase type wrappers; Doh left out tempdir bug; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Tree drawing modules; Use the new Phylip base wrapper; Doc + code formatting cleanup; Use tempdir to run things; Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly; First stab at configuration files for managing version difference of phylip; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming to run method; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: Seqboot wrapper, only working with v3.5 currently; Changes to allow multiple alignments, matrices; Moving executable method to Wrapper base, removing global TMP variables where possible; Handle interleaved output from phylip 3.6, handle 3.6 in general; Remove debugging code; Allow more than one alignment; No more "Using a hash as a reference is deprecated" warnings; Support new exported Menu variable

Bio::Tools::Run::PiseApplication: Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Email not mandatory anymore in Pise; Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.; - Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-); Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::CSR: Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::Puzzle: Pise Factory and Application classes : files associated with each program defined in Pise.; Puzzle interface update : - Add missing amino-acid substitution models. - Alignment file is now set on the command line.

Bio::Tools::Run::PiseApplication::abiview: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; - Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-); Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Pise files update for program beginning with d, e, f and g.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removing application LGICSEARCH upon request of the author

Bio::Tools::Run::PiseApplication::lindna: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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 Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::most: Pise Factory and Application classes : files associated with each program defined in Pise.

Bio::Tools::Run::PiseApplication::mreps: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::PiseApplication::pima: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise: added quicktree, bug fix in PiseJob.pm; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation + location parameter update. Programs from n to r.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs using 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: Pise Factory and Application classes : files associated with each program defined in Pise.; Documentation update and location parameter. Programs from s to z.; Removed all references to submitting bugs 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: Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page; Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).; Clean up to make -w clean; User agent version and job stdout/stderr mtd name; Pise: added quicktree, bug fix in PiseJob.pm; Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.; - Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-); Removed module specific $VERSION, all modules now use global one from Bio::Root::Version; Reverting change for VERSION for 1.2.2 release; 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/.

Bio::Tools::Run::PiseJobParser: Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page; Pise: added warning handling in parser; Clean up to make -w clean; Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.; Removed all references to submitting bugs 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: Wrapper for Primate, Guy Slater's exact match finder; Modified how target and queries are fed; Fix tempdir bug; Make sure resources are freed; Changed to seqname to seq_id; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Removed all references to submitting bugs 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

Bio::Tools::Run::Prints: Make sure resources are freed; Executable name change; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Removed all references to submitting bugs 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: Wrapper module for Profile; Make sure resources are freed; Name of program is pfscan; Add an Id header; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Use seq_id; Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Bio::Tools::Run::Promoterwise: Initial check in for promoterwise; Group hsps together as subseqfeatures; Using parser; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Pseudowise: Added fixes and executable checking; Make sure resources are freed; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Changed the parser to store the ka/ks ratio; Make quieten test work; Remove Kiran's hardcoded path to exe; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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::RemoteBlast: Pure perl (via HTTP) Remote blast submission and retrieval -- see test script for example usage; Quieter tests when verbose == 0, use tempfile for HTML -> text cleanup; Fixed tempfile filehandle handling in retrieve_blast().; Updated to use ncbi Blast.cgi script rather than blast.cgi Text formatting done by cgi rather than HTML tag stripping in module code; Status set to invalid on a failed retrieval; Documentation for retrieve_blast method; Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.; Better synopsis and doc update; Merge main trunk changes which include using SearchIO by default and a better SYNOPSIS; SYNOPSIS needed -readmethod argument; Added example to set MATRIX_NAME and NCBI URL for CGI parameters; Matthew's Changes committed: Add support to save_output. Add fix to put fasta header into QUERY line so query output has Query name. Add support to accept PROGRAM, DATABASE, EXPECT vars like MATRIX_NAME, etc.; Fix synopsis example for save_output, doesn't take rid.; Update SYNOPSIS code so that it runs; Change QUERY to use sequence display_id rather than primary_id; Remove commented lines, minor cleanup of header; Free resources; Moving remote blast into core

Bio::Tools::Run::RepeatMasker: Alpha Wrapper for RepeatMasker; Use the determined path to RP when attempting to find the version; Doc fix; POX fixes; Returns SeqFeature::Generic aot FeaturePair; Brought module in-line with new WrapperBase; Returns FeaturePairs now; Dump tempdir bug; Fixed nasty bug coming from Ensembl missing the first line of repeatmasker output file; Tiny extra curly brace; Moving parsing code out of wrapper; Make sure resources are freed; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Move quiet to a wrapper param; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Cleaned docs for cleanup(); Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: Wrapper module for seg program; Wrapper module for Seg(Documentation changes); Make sure resources are freed; Can run tests if we let executeable find the exe; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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: wrapper for signalp; Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; Bug fix caught by david, truncate sequence to 50 aa; 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::StandAloneBlast: Migrated code that runs tools to Bio::Tools::Run; Renaming packages for new dir structure; Fixed to PROPER usage of tempfile; Migrated to new Bio::Root::RootI chained new; Fixed several doc format bugs. (Why is an unprotected -p in the DESCRIPTION section disallowed and somewhere else it is not? Anyway, perldoc is quiet now.); Fixed inclusion of 'use Bio::Root::RootI' instead of Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).; Updated bptutorial and other documentation; BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes; Changed to adopt Bio::Root::IO.; Io was not initialized, meaning tempfiles were not cleaned up - better argument matching; Intitialize io -- facilitate tempfile cleanup; Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.; Rewrote exists_blast(). Should now work properly on both Unix and MSWin.; Merged over exists_blast() rewrite and other fixes from the main trunk.; Fix to avoid bark in File::Spec.; Small fix to shut up File::Spec.; Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.; Nice message printing when blast is not runnable; Find blast executeable in the PATH if possible -- bl2seq might still fail if one does not have .ncbirc set correctly; Use SearchIO not Tools::Blast; Call cleanup upon _setinput call; Io cleanup called at outset of an analyses -- from branch; Merge cleanup io from main trunk; StandAlone tests will detect that data dir is not set and exit test nicely; Remove debug code and tests for blastinstalled more efficiently; Merge changes from branch; Minor documentation fixes; Explicitly closing some filehandles appears to do a better job freeing resources; Convert StandAloneBlast to WrapperBase (finallyperl -I. -w t/StandAloneBlast.t) -- need to test in different environments now; Fixed Issue #1354 from bugzilla, improved test to report more error details; This is really what I meant by splitting up these conditionals - careful about blindly committing submitted patches; Made docs slightly more clear (still long ways to go IMHO); Deal with changes needed as seen by Issue #1359, mostly this is just a needed map_chars call in StandAloneBlast but have cleaned up the code some in other places; Moving standaloneblast from bioperl-run

Bio::Tools::Run::Tmhmm: Wrapper module for Tmhmm(Documentation changes); Insure filehandles are closed; Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;); Moving executable method to Wrapper base, removing global TMP variables where possible; Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.; Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen; 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/.

Bio::Tools::Run::TribeMCL: Wrapper for tribemcl program for protein family clustering using markov flow simulation based on blast scores; Modified the way input is fed.; Takes in HSP as well; More robust program finding; Print data to file right away rather than holding array in memory - there appeared to be a memory leak otherwise anyways with the simple blast file parsing returning an array ref.; Inherit from WrapperBase, inline with ProtML; Added consensus description generation, with dependency on Algorith::Diff; Brought up to spec with the new Objects and seqname --> seq_id transition Don't use my %hash = undef; we get warnings, initialize to () Also insuring that tmp filehandles are closed to insure freeing of resources; Forgot to commit; Separated parameters for tribe-matrix and mcl in MATRIXPROGRAM_PARAMS and MCLPROGRAM_PARAMS. To discriminate upper and lower case parameters, in particular for mcl, AUTOLOAD is case sensitive when for unallowed parameters. Changed as consequences the way to build the command line in _run_matrix and _run_mcl methods. in _consensifier make sure that UNKNOWN has confidence_annotation_score equal to 0.; Checks to quieten tests; Do require for Algorithm::Diff; Moving executable method to Wrapper base, removing global TMP variables where possible; 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/.

Bio::Tools::Run::Vista: Vista wrapper taking in SimpleAlign object and generate pdfs; Support more options; Bug, don't reverse seq; More docs; 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/.

Makefile.PL: Makefile; Prompt user when Makefile.PL is run; Makefile.PL with sub_test option; Skipping Pise tests if XML::Parser::SAX not installed, added dependency in Makefile; SAX/Sax -> PerlSAX; Added dependency to HTML::PArser which caused Pise tests to fail if not present; Added Algorithm::Diff dependency for TribeMCL; VERSION to 1.2.2; George Hartzell fixes; Version updates

examples/pise/blast-kun.pl: Added examples for running blast2 and phylogeny on a non-default Pise server.

examples/pise/blast2.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Pise: added data for examples

examples/pise/clustalw.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

examples/pise/dnadist.data: Pise: added data for examples

examples/pise/dnadist.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Pise: added data for examples

examples/pise/genscan.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run; Pise: added data for examples

examples/pise/needle.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

examples/pise/phylo-kun.pl: Added examples for running blast2 and phylogeny on a non-default Pise server.

examples/pise/toppred.pl: Added t and examples directories together with Pise files; Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

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/panalysis.PLS: Added a general Analysis client together with its incarnation as a SOAP client; Added -timeout parameter to the SOAP-based Analysis client; Changes in Soaplab API; 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: Added a general Analysis client together with its incarnation as a SOAP client; Changes in Soaplab API; 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/run_neighbor.PLS: Some scripts for running protdist and neighbor, for easy use in the bsub world

scripts/run_protdist.PLS: Some scripts for running protdist and neighbor, for easy use in the bsub world

Run 1.4.0 1.5.1 delta

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