how to use GTR+G+I in MCMCTree?

[Cathy]

Hi,

I'm new to PAML. I have several questions for MCMCTree.

1. Can I use baseml likelihood tree directly in MCMCTree? Or I have to re-call baseml in MCMCTree?

2. I used GTR+G in baseml (I planned to use GTR+G+I in baseml, but baseml doesn't allow using invariant model. So I ended up with using GTR+G). I want to use the same model, GTR+G in MCMCTree. However, I didn't find GTR or REV model in the .clt file. Can anyone help me?

3. Does MCMCTree allow using invariant model?

Thank you in advance!

Regards,

Cathy 

[Asif]

1. Can I use baseml likelihood tree directly in MCMCTree? Or I have to re-call baseml in MCMCTree?

mcmctree requires rooted bifurcating tree topology (no branch lengths). You can annotate tree with fossil calibrations.

 

2. I used GTR+G in baseml (I planned to use GTR+G+I in baseml, but baseml doesn't allow using invariant model. So I ended up with using GTR+G). I want to use the same model, GTR+G in MCMCTree. However, I didn't find GTR or REV model in the .clt file. Can anyone help me?

I think HKY is the most complex model that can be used.

 

3. Does MCMCTree allow using invariant model?

No.

Please see PAML documentation: http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf