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

Ryan Golhar golharam at umdnj.edu
Thu Jun 22 17:05:00 EDT 2006


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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