Changes for version 1.7.3
- The following modules have been moved to the BioPerl distribution so that new BioPerl Run tools can be developed without being dependent on the whole BioPerl-Run distribution:
- Bio::Tools::Run::Analysis Bio::Tools::Run::AnalysisFactory Bio::Tools::Run::Phylo::PhyloBase Bio::Tools::Run::WrapperBase Bio::Tools::Run::WrapperBase::CommandExts
- The following modules have been removed from BioPerl-Run to be part of separate distributions and have independent development:
- Bio::Tools::Phylo::Gumby Bio::Tools::Run::AssemblerBase Bio::Tools::Run::BWA Bio::Tools::Run::BWA::Config Bio::Tools::Run::Bowtie Bio::Tools::Run::Bowtie::Config Bio::Tools::Run::Cap3 Bio::Tools::Run::Maq Bio::Tools::Run::Maq::Config Bio::Tools::Run::Meme Bio::Tools::Run::Minimo Bio::Tools::Run::Newbler Bio::Tools::Run::Phrap Bio::Tools::Run::Phylo::Gumby Bio::Tools::Run::TigrAssembler
- New program previously part of the BioPerl distribution:
- bp_blast2tree
- All Bio::Installer modules and the bioperl_application_installer script have been removed. These were unsafe and out of date. Use a package manager of your choice to install external programs.
Documentation
builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
Modules
Client for the NCBI Entrez EUtilities SOAP server
WSDL parsing for Entrez SOAP EUtilities
Interface to the NCBI Entrez web service *BETA*
Handle for Entrez SOAP DocSums
Conversion of Entrez SOAP messages to BioPerl objects
Fetch adaptor for 'seq' efetch SOAP messages
Fetch adaptor for 'taxonomy' efetch SOAP messages
Handle for Entrez SOAP GlobalQuery items
Handle for Entrez SOAP LinkSets
Accessor object for SoapEUtilities results
EMBOSS application factory class
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 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 a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
Wrapper for Pal2Nal
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)
A SOAP-based access to the analysis tools
A SOAP-based access to the list of analysis tools
Run wrapper for the BEDTools suite of programs *BETA*
Configuration data for bowtie commands
A wrapper for NCBI's blast+ suite
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 GERP
Hyphy wrapping base methods
Wrapper for custom execution of Hyphy batch files
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 for footprinting using phastCons
Wrapper for phyloFit
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
a run wrapper for the samtools suite *BETA*
configurator for Bio::Tools::Run::Samtools
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
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
Compute with NCBI's blast+ suite *ALPHA*
Provides BLAST methods to StandAloneBlastPlus
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
Object for the local execution of WU-Blast.
Object for identifying transmembrane helixes in a given protein seequence.
Wrapper for Vista
Wrapper for local execution of tRNAscan-SE
Provides
in lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
in lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
in lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm
in lib/Bio/Tools/Run/Analysis/soap.pm
in lib/Bio/Tools/Run/BlastPlus/Config.pm