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

[Bingshan Li]

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!