[Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML package)
golharam at umdnj.edu
Sat Jun 24 14:57:52 EDT 2006
It looks like DNAStatistics is only for coding sequences. I'm trying to
calculate the Ks of exons and the K (or Ki) of introns. All the methods
in bioperl are based on coding sequences. Only the PAUP package (that
I've found) does non-coding sequences. I would have used it but you
need to pay for it and we don't have the funding to purchase much at the
I brielfy looked at PHYLIP and EMBOSS but it didn't look as
straight-forward as I was hoping it would be. Either that, or I was
getting fustrated looking for a simple solution.
In the end, I found a molecular evolution book that talks about several
methods used for non-coding sequences so I went ahead and implemented
them. They seem to work well.
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
Sent: Saturday, June 24, 2006 2:43 PM
To: golharam at umdnj.edu
Cc: bioperl-l at lists.open-bio.org; 'Alisha Holloway'
Subject: Re: [Bioperl-l] Bio::Tools::Phylo::PAML with (baseml from PAML
You should look at the Align::DNAStatistics module if you just want
pairwise DNA distance. I put in several different distance methods.
Or you can use the distance methods implemented in PHYLIP or EMBOSS
programs -- I thought you wanted the somewhat more sophisticated ML
approaches that are implemented in PAML?
On Jun 24, 2006, at 10:43 AM, Ryan Golhar wrote:
> I've managed to code three methods to calculate K into a perl script
> using the algorithms as described in "Molecular Evolution" by Wen-
> 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
> 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
> 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-
>> 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
>> 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
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Jason Stajich
> Duke University
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