About initial length of input tree in TestNH

[Giap Nguyen]

Dear all

 

In TestNH package, the option for tree length is "init.brlen.method = Input". To my understand, brlen defined in TestNH is measured in number of substitutions of nucleotide, not in codon. In PAML package, the branch length used is measure in substituitions/codon. So, is it somehow incongruent between TestNH and PAML in measuring dN/dS?

 

Thank you very much!

Best regards

Giap Nguyen

[Julien Yann Dutheil]

Hi Nguyen,

For the branch lengths units, Laurent can answer better than me. In
any case, this does not affect the inference of omega values.

Best,

Julien.

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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