Anyone know of a program or R package which I could use to quickly tally up the most common topologies from a series of bootstrap pseudorep trees, or from trees sampled from a posterior distribution?
For example I would like to have something like the following output:
((1, 2), (3, 4), 5) 80
(1, (2, 3), (4, 5)) 17
(4, (1, 2), (3, 5)) 3
With each topology tallied up. I think I could script it without too much difficulty, but thought maybe there was something already made which could save me some time. Thanks in advance
Dear Tyler Chafin,
Look the link. May be useful.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853548/
http://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-02-5043
Regards, Shafagat
If you are using NJ, ML or MP, then the 'ape' and 'phangorn' packages for R are very useful. I have used both extensively. As far as I am aware there are no good BI phylogenetic packages for R.
Hey, I'm not sure if this helps, but if you manage to load your sampled trees into DENSITREE, it will give you a graphical output of the different topologies, including the number of trees per topology. It comes in the BEAST package but works fine for .tre files output by MrBayes as well.
Cheers, tom
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