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

Ryan Golhar golharam at umdnj.edu
Sat Jun 24 14:57:52 EDT 2006


Hi Jason,

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
moment.

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.  

Ryan


-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
Stajich
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
package)


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?

--jason

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- 
> 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
> Stajich
> 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
> package)
>
>
> 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
> work+PAML.
>
> -jason
> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12



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