[Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML package)

Chris Fields cjfields at uiuc.edu
Fri Jun 23 10:58:24 EDT 2006

***sounds of crickets***


It's a pretty good possibility that Jason and the rest are on the road to
conferences and such.  There's been mention of a Durham, NC meeting and, of
course, YAPC is happening soon as well.  I wish I could help but I know
diddly about PAML besides the HOWTO on the wiki (though I may be using it
myself soon).  Sorry, you may have to be a bit patient for a more productive


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ryan Golhar
> Sent: Thursday, June 22, 2006 4:05 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML
> package)
> Hi all,
> I'm trying to use Bio::Tools::Phylo::PAML to parse the results from
> baseml in the PAML package to measure the distances of some non-coding
> regions.
> I started with the coding regions, and used the script
> bp_pairwise_kaks.pl without much trouble.  Now, I'm trying to do
> something similar for non-coding regions.  However, when I call
> Bio::Tools::Phylo::PAML::Result->get_MLmatrix(), I'm getting 'undef'
> meaning matrix was never defined.
> I wanted to find out if anyone on here has done this before or knows a
> way to measure substitution frequencies of non-coding regions with the
> PAML package.  The documentation with PAML is sparse so I'm not sure how
> to interpret its output directly - that's why I'm using Bioperl.
> Hopefully someone can help me before I start digging into the
> code...Thanks.
> Ryan
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