Author image Sendu Bala
and 1 contributors

Modules

EMBOSS application factory class
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
DESCRIPTION of Object UNAUTHORIZED
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program UNAUTHORIZED
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.
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program UNAUTHORIZED
Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
run the MAFFT alignment tools UNAUTHORIZED
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program UNAUTHORIZED
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program UNAUTHORIZED
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program UNAUTHORIZED
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 class to create Pise application objects.
A SOAP-based access to the list of analysis tools
wrapper for Cap3 UNAUTHORIZED
wrapper for ncoils program
class for EMBOSS Applications
class for EMBOSS Application qualifiers
Object for execution of the Eponine which is a mammalian TSS predictor
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 hmmsearch ,hmmbuild, hmmcalibrate, hmmalign, hmmpfam
run java programs
Perl extension for Mdust nucleotide filtering
a wrapper for running Phrap UNAUTHORIZED
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. UNAUTHORIZED
A wrapper for the Molphy pkg app ProtML
Wrapper aroud the PAML program baseml UNAUTHORIZED
Wrapper aroud the PAML program codeml
Wrapper aroud the PAML program evolver UNAUTHORIZED
Wrapper aroud the PAML program yn00
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
A class manage Pise programs information, configuring parameters and submit jobs.
A class to manage Pise jobs.
A class to parse a Pise server XHTML output.
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 RepeatMasker Program
Object for identifying low complexity regions in a given protein seequence.
Object for identifying transmembrane helixes in a given protein seequence.
Wrapper for Vista

Provides

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