I'd like to combine boostraps/priors from multiple phylogenetic trees onto a reference tree topology. The trees would contain identical set of taxa (tip labels) and distinct node/branch values. In the resulting tree, the node/branch information from the trees should be saved into the reference tree node/branch label and in case there is a conflict, this should be further labeled.
Currently this functionality is available in a program with GUI: TreeGraph2 (conflict is labeled by surrounding the value of the conflicting branch value in square parentheses). However, it is laborious to combine multiple trees (a lot of clicking) and it is not possible (as far as I know) export a tree in newick format which would contain the combined node/branch labels. Do you know about any alternatives? R package would be great, but any suggestion is welcome. Thanks!
Maybe the consensus() function in the R package ape does what you need.
I think consensus() is not doing what I'm looking for here - to compare a reference tree with a set of some other trees and generate a tree with the same topology as the reference tree but additionally containing conflict/support information accumulated from all the other input trees.