[Seqinr-forum] seqinr problem

[Leonor Palmeira]

Dear JLA,

the documentation for the kaks() function (that you can access by ?kaks) 
answers your question:

"When the alignment does not contain enough information (_i.e._ close to 
saturation), the Ka and Ks values are forced to 10."

I suspect your sequences are too divergent for a KaKs analysis and I'm 
afraid changing the calculation method will not improve your data...
For now, the only KaKs method implemented in *seqinr* is indeed Li (1993).

Best,
Leonor.

On 15/11/10 17:11, José Luis Abal Fabeiro wrote:
> Hi,
>
> I have a problem with the *seqinr* package because I have Ks values
> equal to 9.999999 ... I don´t know if this is a bug of the software or
> is a calculation limit of Li's method (1993). Could you help me? And if
> this a limit of Li's method, do you know another way to calcute on R the
> values of Ks and Ka, like the Nei and Gojobori method? or in other
> softwares using multiple files?
>
> Thank you very much!
>
> JLA
>
> If you want I can send you the alignment of this Ks value ....