I have a set of trees (e.g., MrBayes output *.runX.t) with many taxa: A, B, C, .... Z.
I need to infer statistical support for a certain clade ((E,F),G).
Sumtrees (Dendropy package) is a useful tool, but AFAIK the only thing it can provide in my case is the cumulative number of trees which contain ((E,F),G), or (E,(F,G)), or (E,F,G).
Is it possible to get a number of trees with the exact clade ((E,F),G) excluding trees with (E,(F,G)) or (E,F,G)?
Thank you in advance.
I think you should have a look on the ete3 package if you are familier with command line. It is a python package. It is very good package for phylogenetic analysis, and can do extract a part tree as you want to do.
Hello,
It seems to me that what you want to do is testing a clade topology rather than just the clade itself. To do that you can perform log-likelihood tests (e.g. Shimodaira-Hasegawa test implemented in PAUP).
All the best,
Olivier
A very simple way was proposed by Joe Healey https://www.biostars.org/p/241525/ : open the set of trees in a text editor and check how many times the string ((E,F),G) is found.
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