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<div class="moz-cite-prefix">Dear Trevor,<br>
<br>
just in case, more information on the way kaks is calculated can
be found with:<br>
<br>
help(seqinr)<br>
<br>
<br>
All the best,<br>
<br>
Simon<br>
<br>
<br>
<br>
<br>
Le 22/11/12 10:30, Simon Penel a écrit :<br>
</div>
<blockquote cite="mid:50ADF0A0.7070604@univ-lyon1.fr" type="cite">Dear
Trevor,
<br>
<br>
I am not using seqinr on a regular basis, so I am not sur I can
help about this problem.
<br>
<br>
Concerning the way ka ks is calculated you may find the
information here:
<br>
<br>
<a class="moz-txt-link-freetext" href="https://r-forge.r-project.org/scm/viewvc.php/pkg/src/kaks.c?view=markup&root=seqinr">https://r-forge.r-project.org/scm/viewvc.php/pkg/src/kaks.c?view=markup&root=seqinr</a>
<br>
<br>
(or directely in the sources of seqinr if you download it at
<a class="moz-txt-link-freetext" href="http://cran.r-project.org/web/packages/seqinr/index.html">http://cran.r-project.org/web/packages/seqinr/index.html</a>)
<br>
<br>
Does the problem occurs with the example given in seqinr :
<br>
<br>
s <- read.alignment(file = system.file("sequences/test.phylip",
package = "seqinr"), format = "phylip")
<br>
kaks(s)
<br>
<br>
<br>
All the best,
<br>
<br>
Simon
<br>
<br>
<br>
<br>
Le 21/11/12 20:24, Trevor Krabbenhoft a écrit :
<br>
<blockquote type="cite">Hello,
<br>
<br>
I am looking for clarification on how Ka and Ks are calculated
in the kaks
<br>
function. If I calculate by hand using formulas from Li 1993,
i.e.:
<br>
<br>
Ka = (Ao + (LoBo + L2B2))/(Lo + L2)
<br>
<br>
Ks = (L2A2 + L4A4)/(L2 + L4) + B4
<br>
<br>
I obtain different answers than if I pull out ka and ks using
$ka and $ks
<br>
<br>
e.g.,
<br>
<br>
test.k<-kaks(myalignment)
<br>
test.k$ka #ka is different here than what I calculate by
hand using
<br>
$A0, $L0, $B0, etc.
<br>
<br>
#The details are buried in the kaks function in C - is there a
way to 'see'
<br>
how it is calculating these? Which should I use if I want to
follow Li's
<br>
method?
<br>
<br>
#Thank you for any insight.
<br>
<br>
#Trevor
<br>
<br>
<br>
<br>
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<br>
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<br>
</blockquote>
<br>
<br>
<br>
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<br>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
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
<a class="moz-txt-link-freetext" href="http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr">http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr</a>
ATTENTION NOUVELLE ADRESSE:
<a class="moz-txt-link-abbreviated" href="mailto:simon.penel@univ-lyon1.fr">simon.penel@univ-lyon1.fr</a>
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