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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Nov 1 18:08:04 EST 2005

> 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.

I don't know anything about the details of those ratios, but I do notice
	1.35 = (1/2) / 0.37 

if that helps. 

Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium

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