bioperl-run-1.4 - Wrapper for Vista - metacpan.org

Modules

Bio::Factory::EMBOSS

EMBOSS appliaction factory class

Bio::Tools::Run::Alignment::Blat

Bio::Tools::Run::Alignment::Clustalw

Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program

Bio::Tools::Run::Alignment::DBA

Object for the alignment of two sequences using the DNA Block Aligner program.

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

Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)

Bio::Tools::Run::Alignment::Sim4

Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences

Bio::Tools::Run::Alignment::StandAloneFasta

Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)

Bio::Tools::Run::Alignment::TCoffee

Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program

Bio::Tools::Run::Analysis

Module representing any (remote or local) analysis tool

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

A SOAP-based access to the analysis tools

Bio::Tools::Run::AnalysisFactory

A directory of analysis tools

Bio::Tools::Run::AnalysisFactory::Pise

A class to create Pise application objects.

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

A SOAP-based access to the list of analysis tools

Bio::Tools::Run::Coil

Bio::Tools::Run::EMBOSSApplication

class for EMBOSS Applications

Bio::Tools::Run::EMBOSSacd

class for EMBOSS Application qualifiers

Bio::Tools::Run::Eponine

Object for execution of the Eponine which is a mammalian TSS predictor

Bio::Tools::Run::FootPrinter

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(for appropriate organisms).

Bio::Tools::Run::Hmmer

Wrapper for local execution of hmmsearch ,hmmbuild, hmmcalibrate, hmmalign, hmmpfam

Bio::Tools::Run::Hmmpfam

Bio::Tools::Run::Mdust

Perl extension for Mdust nucleotide filtering

Bio::Tools::Run::Phylo::Molphy::ProtML

A wrapper for the Molphy pkg app ProtML

Bio::Tools::Run::Phylo::PAML::Codeml

Wrapper aroud the PAML program codeml

Bio::Tools::Run::Phylo::PAML::Yn00

Wrapper aroud the PAML program yn00

Bio::Tools::Run::Phylo::Phylip::Base

Base object for Phylip modules

Bio::Tools::Run::Phylo::Phylip::Consense

Wrapper for the phylip program Consense

Bio::Tools::Run::Phylo::Phylip::DrawGram

use Phylip DrawTree program to draw phylograms or phenograms

Bio::Tools::Run::Phylo::Phylip::DrawTree

use Phylip DrawTree program to draw trees

Bio::Tools::Run::Phylo::Phylip::Neighbor

Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate.

Bio::Tools::Run::Phylo::Phylip::PhylipConf

Bio::Tools::Run::Phylo::Phylip::ProtDist

Wrapper for the phylip program protdist

Bio::Tools::Run::Phylo::Phylip::ProtPars

Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object

Bio::Tools::Run::Phylo::Phylip::SeqBoot

Wrapper for the phylip program SeqBoot

Bio::Tools::Run::PiseApplication

A class manage Pise programs information, configuring parameters and submit jobs.

Bio::Tools::Run::PiseApplication::CSR

Bio::Tools::Run::PiseApplication::Puzzle

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bio::Tools::Run::PiseApplication::most

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bio::Tools::Run::PiseApplication::sirna

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

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

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

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

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

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

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

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

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

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

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

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

Bio::Tools::Run::PiseApplication::tranalign

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

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

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

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

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

Bio::Tools::Run::PiseApplication::twofeat

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

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

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

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

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

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

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

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

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

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

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

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

Bio::Tools::Run::PiseJob

A class to manage Pise jobs.

Bio::Tools::Run::PiseJobParser

A class to parse a Pise server XHTML output.

Bio::Tools::Run::PiseWorkflow

Bio::Tools::Run::Primate

Bio::Tools::Run::Primer3

Create input for and work with the output from the program primer3

Bio::Tools::Run::Prints

Bio::Tools::Run::Profile

Bio::Tools::Run::Promoterwise

Wrapper for aligning two sequences using promoterwise

Bio::Tools::Run::Pseudowise

Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

Bio::Tools::Run::RepeatMasker

Wrapper for RepeatMasker Program

Bio::Tools::Run::Seg

Object for identifying low complexity regions in a given protein seequence.

Bio::Tools::Run::Signalp

Bio::Tools::Run::Tmhmm

Object for identifying transmembrane helixes in a given protein seequence.

Bio::Tools::Run::TribeMCL

Bio::Tools::Run::Vista

Wrapper for Vista

Provides

Bio::Tools::Run::Analysis::Job

in Bio/Tools/Run/Analysis.pm

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

in Bio/Tools/Run/Analysis/soap.pm

Bio::Tools::Run::Analysis::Utils

in Bio/Tools/Run/Analysis.pm

Examples

Other files

To install Bio::Factory::EMBOSS, copy and paste the appropriate command in to your terminal.

cpanm Bio::Factory::EMBOSS

perl -MCPAN -e shell
install Bio::Factory::EMBOSS

For more information on module installation, please visit the detailed CPAN module installation guide.

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