[Seqinr-forum] kaks calculation problem

[Simon Penel]

Dear Trevor,

just in case, more information on the way kaks is calculated can be 
found with:

help(seqinr)


All the best,

Simon




Le 22/11/12 10:30, Simon Penel a écrit :
> 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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>>
>
>
>
>
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-- 
Simon Penel
Laboratoire de Biometrie et Biologie Evolutive
Bat 711 - CNRS UMR 5558 - Universite Lyon 1
43 bd du 11 novembre 1918 69622 Villeurbanne Cedex
Tel:   04 72 43 29 04      Fax:  04 72 43 13 88
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ATTENTION NOUVELLE ADRESSE:
simon.penel at univ-lyon1.fr
       

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