How To Get A Consensus Tree

Question

[Boyang]

Hi, guys

I try to use consens program in PHYLIP package to got a consensus tree. At the last, I got a tree only with the support values for each branch. But I can not get any information about the average distance between leafs. So how to get the average distance of the consensus tree from a set of trees?

Thanks for your help!!!!

Answer 1

[Eric T.]

Try using a tree distance measure (e.g. Robinson-Foulds distance) between the consensus tree and each of the input trees individually. Then, you'll have N data points for N input trees, and you can calculate the mean, median, and any other statistics you want from it.

(These values may also be interesting to plot or identify outliers among the input trees, especially if the inputs are gene trees and the consensus is supposed to be a species tree.)