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