Orphan modules

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))