HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
Methodology Questions >> How to >> Testing molecular clock http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1373825617 Message started by Nick1979 on Jul 14th, 2013 at 11:13am |
Title: Testing molecular clock Post by Nick1979 on 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 http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=molclockhm.bf (1 KB | 1
)
|
Title: Re: Testing molecular clock Post by Nick1979 on Jul 14th, 2013 at 11:15am
Frgot aqlignment
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=PSEUDOHUMAN10082.txt (1 KB | 0
)
|
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |