Phylogenetic tree support for a user-defined partition

Question

[kshulgina]

Hello,

I am wondering if anyone knows of a phylogenetic software that will allow me to compare the support for a specific partition of species.

More specifically, I am interested in the phylogenetic position of a specific clade X. I want to test whether X is monophyletic with another clade A, monophyletic with another clade B, or whether it is an outgroup to both clades. I want to use a phylogenetic software on some input gene alignment to directly compare how well supported are the different placements of my clade X.

From what I've seen, various phylogenetic softwares like PhyML and MrBayes, show branch support only for partitions in the consensus tree. Is there is some software that will allow me to test the support for a partition of my choosing?

Thanks

Answer 1

[Jean-Karim Heriche]

Have a look at the R package ape, e.g. the boot.phylo() function.

Answer 2

[Joseph Hughes]

There are several ways of doing this phylogenetically. You could for example constrain the topology with X as part of clade A and caulclate the likelihood of the tree, then repeat for X as part of B and then do a likelihood ratio test to see whether the trees are significantly different. You can do this in PhyML. Another approach would be to look at leaf and node stability in the trees produced during a MrBayes run. Alternatively, you could use TreeAnnotator (part of BEAST) to get the bootstrap or posterior probabilities summarised on a topology of your choosing.