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

Alisha Holloway akholloway at ucdavis.edu
Mon Jun 26 00:15:16 EDT 2006


Hi Ryan & Jason,

Sorry I didn't get back to you sooner.  I escaped the central valley 
heat (108!) and went to the coast for the weekend.  I do have a 
script that will call baseml and then parse the results.  Here it is 
and, Ryan, I can show you how to retrieve other parts of the data as 
well, but you may already know how to do this.  I know it's ugly, I 
got it working and didn't clean it up.  Just let me know if you need 
more info.

Alisha

At 11:05 PM -0400 6/24/06, Ryan Golhar wrote:
>  >>they make no assumption about coding sequence,
>>>where do you get that impression
>
>I get that information from the 1.5 api docs:
>
>http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/
>
>Its documented under the description section. 
>
>Oh well, I have it coded and working...might as well use it.
>
>Ryan
>-----Original Message-----
>From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
>Stajich
>Sent: Saturday, June 24, 2006 9:38 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)
>
>
>they make no assumption about coding sequence,where do you get that 
>impression.  the ka,ks are for coding but the tamura/nei kimura, 
>jukes-cantor are all for any type of sequence.
>
>the phylip and emboss are pretty straightforward IMHO - you give it 
>an alignment and you get out a matrix of pairwise numbers....
>\
>but whatever makes sense to you - we are using the same methods as 
>are in Li's book (that is where I took the equations from).
>-j
>On Jun 24, 2006, at 2:57 PM, Ryan Golhar wrote:
>
>>  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
>>
>
>--
>Jason Stajich
>Duke University
>http://www.duke.edu/~jes12


-- 
Alisha Holloway

Postdoctoral Fellow
Section of Evolution & Ecology
3347 Storer Hall
University of California
Davis, CA  95616

530-754-9551 Office
512-297-3958 Cell
530-752-1449 Fax
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