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bioperl::run

Version: 1.2.2

abiview.pm

addquart.pm

align2model.pm

alistat.pm

Bio::Tools::Run::Analysis - Module representing any analysis tool

Bio::Tools::Run::AnalysisFactory - A directory of analysis tools

antigenic.pm

assp.pm

backtranseq.pm

bambe.pm

banana.pm

Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

bionj.pm

biosed.pm

bl2seq.pm

blast2.pm

Blat.pm

blimps.pm

blimps_block.pm

blimps_matrix.pm

boxshade.pm

btwisted.pm

cai.pm

cap.pm

cds.pm

chaos.pm

charge.pm

checktrans.pm

chips.pm

cirdna.pm

clique.pm

Clustalw.pm

clustalw.pm

clustalw_convert.pm

codcmp.pm

Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml

coderet.pm

codnocod.pm

codontree.pm

codonw.pm

Coil.pm

comalign.pm

combat.pm

compseq.pm

con_filter.pm

confmat.pm

cons.pm

Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense

consense.pm

consensus.pm

cpgplot.pm

cpgreport.pm

CSR.pm

cusp.pm

cutseq.pm

dan.pm

Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program.

dca.pm

decorate.pm

degapseq.pm

descseq.pm

dialign2.pm

diffseq.pm

digest.pm

distmat.pm

distquart.pm

dnadist.pm

dnapars.pm

dollop.pm

domainer.pm

dotmatcher.pm

dotpath.pm

dottup.pm

Bio::Tools::Run::Phylo::Phylip::DrawGram - use Phylip DrawTree program to draw phylograms or phenograms

drawgram.pm

drawpyr.pm

Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees

drawtree.pm

dreg.pm

druid.pm

dsc.pm

dssp.pm

einverted.pm

Bio::Factory::EMBOSS - EMBOSS appliaction factory class

Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers

Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

emma.pm

emowse.pm

environ.pm

Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor

eprimer3.pm

equicktandem.pm

est2genome.pm

etandem.pm

extractfeat.pm

extractseq.pm

CGI::FormBuilder::Template::Fast - FormBuilder interface to CGI::FastTemplate

fasta.pm

fastdnaml.pm

fastrna.pm

CGI::FormBuilder::Field - Internally used to create a FormBuilder field

CGI::FormBuilder::Source::File - Initialize FormBuilder from external file

filtersites.pm

findkm.pm

fitch.pm

fmtseq.pm

Bio::Tools::Run::FootPrinter - Wrapper for FootPrinter Program

CGI::FormBuilder - Easily generate and process stateful forms

freak.pm

fuzznuc.pm

fuzzpro.pm

fuzztran.pm

gb2xml.pm

geecee.pm

Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein

Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix.

genscan.pm

getblock.pm

getorf.pm

gff2ps.pm

gibbs.pm

gibbs_scan.pm

golden.pm

grailclnt.pm

gruppi.pm

helixturnhelix.pm

hmmalign.pm

hmmbuild.pm

hmmcalibrate.pm

hmmconvert.pm

hmmemit.pm

hmmer2sam.pm

hmmfetch.pm

Hmmpfam.pm

hmmpfam.pm

hmmscore.pm

hmmsearch.pm

hmoment.pm

homology.pm

CGI::FormBuilder::Template::HTML - FormBuilder interface to HTML::Template

html4blast.pm

iep.pm

infoalign.pm

infoseq.pm

interface.pm

isochore.pm

kitsch.pm

Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools

lassap.pm

lgicsearch.pm

lindna.pm

listor.pm

loadseq.pm

lvb.pm

makehist.pm

map.pm

marscan.pm

maskfeat.pm

maskseq.pm

matcher.pm

Mdust - Perl extension for Mdust nucleotide filtering

megamerger.pm

melting.pm

merger.pm

CGI::FormBuilder::Messages - Localized message support for FormBuilder

mfold.pm

mix.pm

modelfromalign.pm

most.pm

mreps.pm

msa.pm

msbar.pm

mspcrunch.pm

CGI::FormBuilder::Multi - Create multi-page FormBuilder forms

mview_alig.pm

mview_blast.pm

mwfilter.pm

needle.pm

Neighbor.pm

neighbor.pm

newcpgreport.pm

newcpgseek.pm

newseq.pm

njdist.pm

nnssp.pm

notseq.pm

nrscope.pm

nthseq.pm

octanol.pm

oddcomp.pm

palindrome.pm

pam.pm

parciquart.pm

pars.pm

pasteseq.pm

patmatdb.pm

patmatmotifs.pm

patser.pm

pdbsearch.pm

pepcoil.pm

pepinfo.pm

pepnet.pm

pepstats.pm

pepwheel.pm

pepwindow.pm

pepwindowall.pm

pestfind.pm

pftools.pm

phiblast.pm

PhylipConf.pm

pima.pm

Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise application objects.

Bio::Tools::Run::PiseApplication - A class manage Pise programs information, configuring parameters and submit jobs.

Bio::Tools::Run::PiseJob - A class to manage Pise jobs.

Bio::Tools::Run::PiseJobParser - A class to parse a Pise server XHTML output.

plotcon.pm

plotorf.pm

plsearch.pm

polydot.pm

pratt.pm

predator.pm

preg.pm

prettyalign.pm

prettyplot.pm

prettyseq.pm

Primate.pm

primersearch.pm

primo.pm

Prints.pm

prodom.pm

Profile.pm

profit.pm

Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise

prophecy.pm

prophet.pm

prose.pm

prot_nucml.pm

protal2dna.pm

Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip program protdist

protdist.pm

Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML

Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a L<Bio::Tree> object from a multiple alignment file or a SimpleAlign object

protpars.pm

pscan.pm

Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

psiblast.pm

psort2.pm

Puzzle.pm

pyramids.pm

pyreval.pm

qstar.pm

quicktree.pm

readnexus.pm

readseq.pm

recoder.pm

redata.pm

remap.pm

Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program

repeats.pm

restover.pm

restrict.pm

revseq.pm

rnadistance.pm

rnaeval.pm

rnafold.pm

rnaga.pm

rnaheat.pm

rnainverse.pm

rnapdist.pm

rnasubopt.pm

sam2hmmer.pm

sampleseqs.pm

saps.pm

satellites.pm

scan_for_matches.pm

scope.pm

scopparse.pm

Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence.

Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot

seqboot.pm

seqgen.pm

seqmatchall.pm

seqsblast.pm

seqstat.pm

showalign.pm

showfeat.pm

showorf.pm

showseq.pm

shuffleseq.pm

sigcleave.pm

siggen.pm

Signalp.pm

sigscan.pm

silent.pm

Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences

sirna.pm

Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools

CGI::FormBuilder::Source - Source adapters for FormBuilder

splitter.pm

sreformat.pm

StandAloneFasta.pm

stretcher.pm

stride.pm

stssearch.pm

supermatcher.pm

syco.pm

tacg.pm

TCoffee.pm

CGI::FormBuilder::Template - Template adapters for FormBuilder

CGI::FormBuilder::Template::Text - FormBuilder interface to Text::Template

tfscan.pm

tipdate.pm

tmap.pm

Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence.

toppred.pm

tranalign.pm

transeq.pm

treealign.pm

TribeMCL.pm

trimest.pm

trimseq.pm

trnascan.pm

CGI::FormBuilder::Template::TT2 - FormBuilder interface to Template Toolkit

twofeat.pm

unroot.pm

CGI::FormBuilder::Util - Utility functions for FormBuilder

vectorstrip.pm

Vista.pm

water.pm

weighbor.pm

whichdb.pm

wise2.pm

wobble.pm

wordcount.pm

wordmatch.pm

wublast2.pm

xblast.pm

xpound.pm

Bio::Tools::Run::Phylo::PAML::CodeML - Wrapper aroud the PAML program codeml

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