Try phylobayes, for multigene analysis
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Adrian Pelin
Bayesian Phylogeny For Very Divergent Dataset?
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
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Arjen Ten Have
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My question is more directed at whether it will work for divergent datasets...
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Arjen Ten Have
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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.