Changes for version 1.2.2
- o Soaplab
- API changes
- binary input added
- o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
- Numerous documentation fixes in almost all modules
- Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.
- the DESCRIPTION section now contains *only* the parameters that can be set by the client.
- remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface
- new programs sirna, tranalign, twofeat (from EMBOSS 2.6).
- o Bio::Tools::Run::Eponine
- More standardized way of running
- o Bio::Tools::Run::FootPrinter
- Write the files properly
- Mark Wagner's enhancements bug #1399
- o Bio::Tools::Run::Genewise
- more options
- o Bio::Tools::Run::Genscan
- doc fix
- o Bio::Tools::Run::Hmmpfam
- Updated to set params properly and return a SearchIO object
- o Bio::Tools::Run::Mdust
- new location
- Modified to inherit Bio::Tools::Run::WrapperBase
- use Bio::Root::IO to build up paths
- Modified documentation to conform to bioperl format
- o Bio::Tools::Run::Signalp
- uniform sequence truncation lenght
- o Bio::Tools::Run::Vista
- new module
- Support more options
- More documentation
- fix reverse sequence bug
- o Bio::Tools::Run::Phylo::Phylip::SeqBoot
- Allow more than one alignment
- o Bio::Tools::Run::Phylo::Phylip::Neighbor
- Check for multiple data sets and set parameter accordingly
- o Bio::Tools::Run::Alignment::Blat
- moved from Bio::Tools::Run name space
- some code cleanup to avoid warnings and insure filehandles are properly closed, etc
- o Bio::Tools::Run::Alignment::Lagan
- program name included
- small fixes and addition of options
- added the right credits.
- Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
- Quiet declaration warnings
Modules
EMBOSS appliaction factory class
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 local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
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
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).
Perl extension for Mdust nucleotide filtering
A wrapper for the Molphy pkg app ProtML
Wrapper aroud the PAML program codeml
Wrapper aroud the PAML program codeml
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.
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