Correct substitution model for yeast - RAxML

Question

[mschmid]

I have an aligment of multiple genes of yeast mitochondria. It is quite diverse (Candida, Saccharomyces, Yarrowia, etc.)

What protein substitution model would you use to run RAxML on this alignment?

Answer 1

[Sej Modha]

You could use either Prottest for protein alignments or jModelTest for DNA alignments to find out the best model for RAxML.

[DG]

When in doubt something like LG with empirical frequency estimation and gamma rate categories will usually be good enough but prottest is a decent check. I'll also add that in the gran scheme of things, a group of yeast sequences isn't that diverse :)