consensus.edges: Compute consensus edges for a tree under some criterion
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

consensus.edges

R Documentation

Compute consensus edges for a tree under some criterion

Computes consensus edge lengths from a set of input trees using multiple methods.

consensus.edges(trees, method=c("mean.edge","least.squares"), ...)

`trees`	object of class `"multiPhylo"` in which the trees must have edge lengths. This could be, for instance, a sample from the posterior distribution of trees in a Bayesian analysis.
`method`	method for computing the edge lengths. Could be the mean of all trees in which the edge is present, or it could be the least-squares edge lengths computed on the mean patristic distance matrices from the input phylogenies in `trees`. Note that in the latter case the phangorn function `nnls.tree` is used and the option `rooted` will be set to `is.rooted(tree)` for the consensus tree.
`...`	optional arguments, the most popular of which is `consensus.tree` - a user supplied consensus tree. Another optional argument for `method="mean.edge"` is `if.absent` which tells the function how to include absent edges in the computation of average edge lengths. Possible values are `"zero"` (the default) or `"ignore"`.