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

Ryan Golhar golharam at umdnj.edu
Sat Jun 24 10:43:29 EDT 2006

I've managed to code three methods to calculate K into a perl script
using the algorithms as described in "Molecular Evolution" by Wen-Hsuing
Li.   I'd be happy to contribute it as a script...

-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
Sent: Saturday, June 24, 2006 9:40 AM
To: golharam at umdnj.edu
Cc: bioperl-l at lists.open-bio.org list; Alisha Holloway
Subject: Re: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML

baseml is not well-supported to my knowledge - I think I started with  
attempt to capture a small amount of the data in the file.  There are  
some people who have made modifications to possible parse it in-house  
but I know of no submitted patches.   Many of the knowledgeable  
people are probably at the evolution meetings  this week.

I have no idea about the full set of information in the report files  
without going back to the Yang papers first.   It depends on how much  
of that information you really want to capture of just the  
substitution rates.

I'm Ccing Alisha in case she has ideas/solutions from her drosophila  

On Jun 22, 2006, at 5:05 PM, Ryan Golhar wrote:

> 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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Jason Stajich
Duke University

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