[BioRuby] CodeML wrapper for BioRuby

[Michael Barton]

Hi,

I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
'*', which indicate gaps in the alignment. For instance MM*M means that
there is a gap in the alignment in the third sequence.

The changes are in my branch of bioruby.

Thanks

Mike

On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Thank you.
>
> I think PAML programs other than codeml are also valuale
> to write wrappers, especially for baseml and yn00.
>
> In BioPerl, there are four PAML program wrappers.
> (baseml, codeml, evolver, yn00)
>
> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
>
> So, I decide to move the codeml classes under Bio::PAML.
>
> I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> to bio/appl/paml/ and test/unit/bio/appl/paml/.
>
> The reason why I changed CodeML to Codeml is that
> it seems that authors of PAML do not use the word "codeML"
> (the last two letters are uppercase). Indeed, I can't find
> the word "codeML" (or "CodeML") in the PAML's documents.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> On Sat, 16 Aug 2008 18:22:18 +0200
> pjotr2008 at thebird.nl (Pjotr Prins) wrote:
>
> > 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
> > > > > _______________________________________________
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