omega value from N & S counts

[Giap Nguyen]

Dear Dr. Julien Yann Dutheil

 

I found you posted an answer on omega approximation, using R

 

library(ape)
tree.S<-read.phylo("countsS.tree")
tree.N<-read.phylo("countsN.tree")
tree.dNdS<-tree.S
tree.dNdS$edge.length<-tree.N$edge.length / (3 * tree.S$edge.length)
write.phylo(tree.dNdS, file="dnds.tree")

 

I tried on MantellidFrog data, but again, I am afraid I can not reproduce the value as it in MBE paper. In the above command, would you please tell me what does "tree.dNdS<-tree.S" mean?

And would you please tell me (for sure) which one of the two "CountsTree1.dnd" and "CountsTree2.dnd" is synonymous count and nonsynonymous count?

 

Thank you very much!

Best regards

Giap Nguyen

[Julien Yann Dutheil]

Hi,

In this R script, I simply copy the tree.S into tree.dNdS, and then
change the branch lengths to the ratio instead of the S value. tree.S
and tree.N have the same topology, and branches are in the same order,
that's why it is safe to replace the branch lengths by this way.
For the trees, 1 is synonymous, 2 is nonsynonymous (it has smaller
values, typically).
Which stage cannot you reproduce? Are you rerunning the example
programs from the package and find different partitions or omega
values???

J.

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--
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530

§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE