[Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs?
bli1 at bcm.tmc.edu
Mon Oct 31 17:54:13 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.
Thanks a lot!
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