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

Jason Stajich jason.stajich at duke.edu
Tue Nov 1 17:45:16 EST 2005

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  

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

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