Run 1.2.0 1.2.2 delta

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

Bio::Tools::Run::Alignment::Lagan

Added the right credits.

Bio::Tools::Run::Analysis

Binary input added

Removed module specific $VERSION, all modules now use global one from Bio::Root::Version

Bio::Tools::Run::Analysis::soap

Binary input added

Removed module specific $VERSION, all modules now use global one from Bio::Root::Version

Bio::Tools::Run::AnalysisFactory

Removed module specific $VERSION, all modules now use global one from Bio::Root::Version

Bio::Tools::Run::AnalysisFactory::soap

Removed module specific $VERSION, all modules now use global one from Bio::Root::Version

Bio::Tools::Run::FootPrinter

Mark Wagner's enhancements Issue #1399

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

Bio::Tools::Run::PiseApplication::abiview

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::addquart

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::align2model

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::alistat

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::antigenic

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::assp

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::backtranseq

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::bambe

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::banana

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::bionj

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::biosed

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::bl2seq

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::blast2

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::blimps

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::blimps_block

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::blimps_matrix

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::boxshade

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::btwisted

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cai

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cap

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cds

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::chaos

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::charge

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::checktrans

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::chips

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cirdna

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::clique

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::clustalw

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::clustalw_convert

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::codcmp

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::coderet

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::codnocod

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::codontree

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::codonw

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::comalign

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::combat

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::compseq

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::con_filter

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::confmat

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cons

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::consense

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::consensus

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cpgplot

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cpgreport

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cusp

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::cutseq

Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).

Bio::Tools::Run::PiseApplication::dan

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dca

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::decorate

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::degapseq

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::descseq

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dialign2

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::diffseq

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::digest

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::distmat

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::distquart

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dnadist

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dnapars

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dollop

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::domainer

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dotmatcher

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dotpath

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dottup

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::drawgram

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::drawpyr

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::drawtree

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dreg

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::druid

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dsc

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::dssp

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::einverted

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::emma

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::emowse

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::environ

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::eprimer3

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::equicktandem

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::est2genome

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::etandem

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::extractfeat

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::extractseq

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fasta

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fastdnaml

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fastrna

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::filtersites

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::findkm

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fitch

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fmtseq

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::freak

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fuzznuc

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fuzzpro

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::fuzztran

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::gb2xml

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::geecee

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::genscan

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::getblock

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::getorf

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::gff2ps

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::gibbs

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::gibbs_scan

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::golden

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::grailclnt

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::gruppi

Pise files update for program beginning with d, e, f and g.

Bio::Tools::Run::PiseApplication::helixturnhelix

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmalign

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmbuild

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmcalibrate

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmconvert

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmemit

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmer2sam

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmfetch

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmpfam

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmscore

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmmsearch

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::hmoment

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::homology

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::html4blast

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::iep

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::infoalign

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::infoseq

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::interface

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::isochore

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::kitsch

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::lassap

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::lgicsearch

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::lindna

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::listor

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::loadseq

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::lvb

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::makehist

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::map

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::marscan

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::maskfeat

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::maskseq

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::matcher

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::megamerger

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::melting

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::merger

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mfold

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mix

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::modelfromalign

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mreps

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::msa

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::msbar

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mspcrunch

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mview_alig

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mview_blast

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::mwfilter

Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.

Bio::Tools::Run::PiseApplication::needle

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::neighbor

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::newcpgreport

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::newcpgseek

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::newseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::njdist

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::nnssp

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::notseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::nrscope

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::nthseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::octanol

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::oddcomp

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::palindrome

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pam

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::parciquart

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pars

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pasteseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::patmatdb

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::patmatmotifs

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::patser

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pdbsearch

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepcoil

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepinfo

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepnet

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepstats

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepwheel

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepwindow

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pepwindowall

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pestfind

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pftools

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::phiblast

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pima

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::plotcon

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::plotorf

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::plsearch

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::polydot

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pratt

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::predator

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::preg

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prettyalign

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prettyplot

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prettyseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::primersearch

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::primo

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prodom

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::profit

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prophecy

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prophet

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prose

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::prot_nucml

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::protal2dna

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::protdist

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::protpars

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pscan

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::psiblast

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::psort2

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pyramids

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::pyreval

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::qstar

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::quicktree

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::readnexus

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::readseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::recoder

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::redata

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::remap

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::repeats

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::restover

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::restrict

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::revseq

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnadistance

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnaeval

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnafold

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnaga

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnaheat

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnainverse

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnapdist

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::rnasubopt

Documentation + location parameter update. Programs from n to r.

Bio::Tools::Run::PiseApplication::sam2hmmer

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::sampleseqs

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::saps

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::satellites

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::scan_for_matches

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::scope

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::scopparse

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::seqboot

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::seqgen

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::seqmatchall

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::seqsblast

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::seqstat

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::showalign

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::showfeat

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::showorf

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::showseq

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::shuffleseq

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::sigcleave

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::siggen

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::sigscan

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::silent

Documentation update and location parameter. Programs from s to z.

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.

Bio::Tools::Run::PiseApplication::splitter

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::sreformat

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::stretcher

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::stride

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::stssearch

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::supermatcher

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::syco

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::tacg

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::tfscan

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::tipdate

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::tmap

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::toppred

Documentation update and location parameter. Programs from s to z.

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.

Bio::Tools::Run::PiseApplication::transeq

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::treealign

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::trimest

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::trimseq

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::trnascan

Documentation update and location parameter. Programs from s to z.

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.

Bio::Tools::Run::PiseApplication::unroot

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::vectorstrip

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::water

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::weighbor

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::whichdb

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::wise2

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::wobble

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::wordcount

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::wordmatch

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::wublast2

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::xblast

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseApplication::xpound

Documentation update and location parameter. Programs from s to z.

Bio::Tools::Run::PiseJob

Removed module specific $VERSION, all modules now use global one from Bio::Root::Version

Reverting change for VERSION for 1.2.2 release

Bio::Tools::Run::Signalp

Bug fix caught by david, truncate sequence to 50 aa

Makefile.PL

VERSION to 1.2.2

examples/pise/blast-kun.pl

Added examples for running blast2 and phylogeny on a non-default Pise server.

examples/pise/phylo-kun.pl

Added examples for running blast2 and phylogeny on a non-default Pise server.