[BioRuby] CodeML wrapper for BioRuby

[Pjotr Prins]

codeml is, by far, the most valuable tool.

Pj.

On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> Hi Mike,
> 
> The CodeML wrappers is now included in bioruby git.
> http://github.com/bioruby/bioruby/tree/master
> 
> As PAML has some executables other than codeml,
> (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> 
> Is it OK? (or, is codeml the only valuable component to write
> wrapper/parser for bioruby?)
> 
> Do you (or someone) plan to write other PAML's wrappers/parsers?
> 
> Thanks,
> 
> Naohisa Goto
> ngoto at bioruby.org / ng at bioruby.org
> 
> 
> On Fri, 15 Aug 2008 20:15:09 +0900
> Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> 
> > Hi, 
> > 
> > It seems good. It will be included in BioRuby.
> > 
> > In my machine, a test was failed.
> > Can you fix the problem?
> (snip)
> >
> > On Wed, 13 Aug 2008 16:34:20 +0100
> > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > 
> > > Hi,
> > > 
> > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > in BioRuby. The fork is located here
> > > 
> > > http://github.com/michaelbarton/bioruby/tree/master
> > > 
> > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > 
> > > Thanks
> > > 
> > > Mike
> > > _______________________________________________
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > 
> > 
> > _______________________________________________
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> 
> 
> -- 
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