Run 1.2.0 1.2.2 delta

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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.
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