[BioRuby] CodeML wrapper for BioRuby

[Naohisa GOTO]

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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> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


-- 
後藤 直久  ngoto at gen-info.osaka-u.ac.jp
大阪大学微生物病研究所 遺伝情報実験センター ゲノム情報解析分野(安永研)
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