choosing a model for each codon in jModeltest

Question

[sohanasngh]

Hello!

I want to choose a model for each codon in my MSA, but how do I implement this in jModeltest?

Thanks :)

Answer 1

[abascalfederico]

jModelTest does not do selection of models of codon evolution. Do you mean instead, select a model for each codon position (first, second and third)? If that were the case, you should split your alignment in alignments of these positions

[sohanasngh]

Thanks for your answer. How do I split the alignment?

[abascalfederico]

I would write a script for this but there must be software doing this.

You may want to try translatorX. One of the outputs are the position-specific alignments (at the end of the results page)

Hope this helps,