[Seqinr-forum] kaks calculation problem

[Trevor Krabbenhoft]

Hello,

I am looking for clarification on how Ka and Ks are calculated in the kaks
function.  If I calculate by hand using formulas from Li 1993, i.e.:

Ka = (Ao + (LoBo + L2B2))/(Lo + L2)

Ks = (L2A2 + L4A4)/(L2 + L4) + B4

I obtain different answers than if I pull out ka and ks using $ka and $ks

e.g.,

test.k<-kaks(myalignment)
test.k$ka        #ka is different here than what I calculate by hand using
$A0, $L0, $B0, etc.

#The details are buried in the kaks function in C - is there a way to 'see'
how it is calculating these?  Which should I use if I want to follow Li's
method?

#Thank you for any insight.

#Trevor
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