Orphan modules

From BioPerl
Jump to: navigation, search

Contents


Modules which need a friend!

Popular modules which are orphaned as the author no longer wants to feed and care for them. Also check the BioPerl Project priority list.

Core package (bioperl-live)

Bio::Tools::Tmhmm - parse TMHMM output (transmembrane HMM)
Torsten Seemann has adopted this neglected module.
Bio::Tools::Prints
This parser doesn't seem to match up with the PRINTS output I have seen. This module returns Bio::SeqFeature::FeaturePair objects; it should probably be part of the Bio::SearchIO system. --Torsten 02:21, 25 September 2006 (EDT)

(Perhaps the following are better suited to bioperl-run, but too many people want to do BLAST out of the box so we kept them in the Core distribution)

Bio::Tools::Run::StandAloneBlast
Torsten Seemann has taken this on. Thanks very much Torsten.
Bio::Tools::Run::RemoteBlast
Roger Hall has taken this on. This module provides access to the NCBI BLAST service via HTTP.

Run package (bioperl-run)

Bio::Tools::Run::Alignment::Blat
An audit of the command line options needs to be performed, and the constructor needs to accept named parameters. Victor Ruotti has taken this one, thanks very much Victor.
Bio::Tools::Run::Alignment::StandAloneFasta
This module is a wrapper for running FASTA locally.
Bio::Tools::Run::TribeMCL
This module is a wrapper for running TribeMCL in a pipeline.
Bio::Tools::Run::Hmmer
This module wraps running HMMER applications, it could use some auditing that all cmd-line switches are used. Mauricio has taken this one.
Bio::Tools::Run::Phylo::Molphy::ProtML
ProtML is for building phylogenetic trees from protein sequence alignments, there are several other applications in the Molphy package which need wrappers. (I'm planning to take this one in the coming month or so (Jan. 2007))
Personal tools
Namespaces
Variants
Actions
Main Links
documentation
community
development
Toolbox