++ed by:
PROCH
Author image Christopher Fields
and 1 contributors

Modules

EMBOSS application factory class
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Object for the alignment of two sequences using the DNA Block Aligner program.
Wrapper for running gmap.
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program
Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
run the MAFFT alignment tools
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program
Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program.
Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
Module representing any (remote or local) analysis tool
A SOAP-based access to the analysis tools
A directory of analysis tools
A SOAP-based access to the list of analysis tools
wrapper for CAP3
wrapper for ncoils program
class for EMBOSS Applications
class for EMBOSS Application qualifiers
Wrapper for local execution of the ERPIN suite of programs.
A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API.
Object for execution of the Eponine which is a mammalian TSS predictor
wrapper for the FootPrinter program
Wrapper for local execution of the GeneMark family of programs.
Object for predicting genes in a given sequence given a protein
Object for identifying genes in a given sequence given a matrix(for appropriate organisms).
Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.
Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore
Wrapper for MCS
Wrapper for Transfac's match(TM)
Perl extension for Mdust nucleotide filtering
Wrapper for Meme Program
a wrapper for running Phrap
Wrapper for GERP
Wrapper for gumby
Hyphy wrapping base methods
Wrapper around the Hyphy FEL analysis
Wrapper around the Hyphy Modeltest analysis
Wrapper around the Hyphy REL analysis
Wrapper around the Hyphy SLAC analysis
Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1.
A wrapper for the Molphy pkg app ProtML
Wrapper around the Njtree (Njtree/phyml) best program.
Wrapper aroud the PAML program baseml
Wrapper aroud the PAML program codeml
Wrapper aroud the PAML program evolver
Wrapper aroud the PAML program yn00
Wrapper for footprinting using phastCons
Base object for Phylip modules
Wrapper for the phylip program Consense
use Phylip DrawTree program to draw phylograms or phenograms
use Phylip DrawTree program to draw trees
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.
Wrapper for the phylip program protdist
Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
Wrapper for the phylip program SeqBoot
Wrapper for rapid reconstruction of phylogenies using Phyml
Wrapper for rapid reconstruction of phylogenies using QuickTree
Wrapper around the SLR program
Wrapper for Semphy
Create input for and work with the output from the program primer3
Wrapper for aligning two sequences using promoterwise
Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence
Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune
Wrapper for RepeatMasker Program
Object for identifying low complexity regions in a given protein seequence.
Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
Wrapper for local execution of TIGR Assembler v2.0
Object for identifying transmembrane helixes in a given protein seequence.
Wrapper for Vista
Wrapper for local execution of tRNAscan-SE

Provides

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