[Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs?

Bingshan Li bli1 at bcm.tmc.edu
Tue Nov 1 19:00:39 EST 2005

Thanks, Jason, for this reply and the other for Ganbank parser. For  
Yn00, can we pass a slice of alignment to it so that I can calculate  
ka/ks for sliding windows? I ran PAML as a stand alone program but  
never used it in perl script.

Thanks a lot!


On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote:

> I suggest Codeml and YN00 - I assume you are only doing this for  
> pairwise comparisons and not along a tree?
> The dnastats  module calculates Nei-Gojobori so it will be  
> different, but shouldn't be that different so something must be  
> wrong with your code or the module's method.  Maybe you can post a  
> bug to bugzilla.open-bio.org with a clear example of where it is  
> going wrong and we'll take a look.
> I would just use YN00 for most pairwise - you can parse it with  
> Bio::Tools::Phylo::PAML and automate running it with  
> Bio::Tools::Run::Phylo::PAML::Yn00
> -jason
> On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote:
>> Hi all,
>> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio  
>> but I found the result is very different from the output by yn00  
>> in PAML 3.14. I applied "calc_KaKs_pair" function on two sequences  
>> to test it. The difference is pretty big (for one case it gave ka/ 
>> ks=1.35 while yn00 gave 0.37). Does anybody have same experience?  
>> Is there any other methods I can use to calculate ka/ks ratios? I  
>> will also use it to calculate ka/ks in sliding windows.
>> Thanks a lot!
>> _______________________________________________
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> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12

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