How to estimate branch lengths, amino acid frequencies and the best shape parameter for variable rates among sites (alpha)

[Jingliang Kang]

Dear paml community,

Have some kind peoples ever used codeml to estimate the branch lengths, amino acid frequencies and the best shape parameter for variable rates among sites (alpha) by codeml? could you give me some hints for this estimation?

Thanks so much,

Kang

[Sishuo Wang]

i am unsure if codeml allows estimating the frequency so u can use iqtree +g+f or raxml +g+f0 or +g+fc see also their manual but you may also be aware that you may need to fix the tree topology as the same as the one used in paml analysis.

sishuo

[Sishuo Wang]

Dear jingliang,

I think the above was partly wrong by saying "i am unsure if codeml allows estimating the frequency ".

as i understand now, +F can be specified using "model=3" and model=2 is to use the equilibrium freq given in the "aaRatefile".

best,

sishuo