[Seqinr-forum] kaks calculation problem

[Simon Penel]

Dear Trevor,

I am not using seqinr on a regular basis,  so I am not sur I can help 
about this problem.

Concerning the way ka ks is calculated you may find the information here:

https://r-forge.r-project.org/scm/viewvc.php/pkg/src/kaks.c?view=markup&root=seqinr

(or directely in the sources of seqinr if you download it at 
http://cran.r-project.org/web/packages/seqinr/index.html)

Does the problem occurs with the example given in seqinr :

s <- read.alignment(file = system.file("sequences/test.phylip", package 
= "seqinr"), format = "phylip")
kaks(s)


All the best,

Simon



Le 21/11/12 20:24, Trevor Krabbenhoft a écrit :
> 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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-- 
Simon Penel
Laboratoire de Biometrie et Biologie Evolutive
Bat 711 - CNRS UMR 5558 - Universite Lyon 1
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