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Testing molecular clock (Read 1940 times)
Nick1979
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Testing molecular clock
Jul 14th, 2013 at 11:13am
 
Hi,

I am trying to test whether my sequences are evolving under a molecular clock and just looking at one of the results i am under the suspicion that i am doing something wrong. For example below it seems that human and macaca have very different branch lengths but the molecular clock is not rejected



Unconstrained Analysis:
Log Likelihood = -927.267004691088;
Tree myTree=(marmoset:0.124589,macaca:0.0479423,human:0.0258198);


Molecular Clock Analysis:
Log Likelihood = -928.28141233301;
Tree myTree=(marmoset:0.124299,macaca:0.0369108,human:0.0369108);


P-value for Global Molecular Clock Test:0.362617


The example above is based on an alignment of three orthologous non-functional sequences (length 430 excluding gaps) belonging to human, macaca and marmoset. Marmoset is  taken to be the outgroup. I have attached my code and alignment


Thank you

Nicholas



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Nick1979
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Re: Testing molecular clock
Reply #1 - Jul 14th, 2013 at 11:15am
 
Frgot aqlignment
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