Bayesian Phylogeny For Very Divergent Dataset?

Question

[Arjen Ten Have]

A reviewer asked me to complement a maximum likelihood phylogeny with a Bayesian tree. Intuitively I think Bayes has problems with large divergent datasets (similarity below 25%), but intuition does not build papers. Can anybody comment on this? If applicable, which software should I use, MrBayes or Phylobayes? The idea is not to swap, but rather to substantiate the ML trees and provide better statistical support.

Cheers Arjen

[qiyunzhu]

You can translate ML bootstrap values on to a Bayesian tree or any given tree, using RAxML. It will work even if the RAxML tree looks different in topology. I am not sure if the reverse way would work. But theoretically you can translate a Bayesian .t or .trees file onto an ML tree, too.

Answer 1

[Arjen Ten Have]

My question is more directed at whether it will work for divergent datasets...

[Adrian Pelin]

Try phylobayes, for multigene analysis