Weighted compromise trees: a method to summarize competing phylogenetic hypotheses

A new consensus method for summarizing competing phylogenetic hypotheses, weighted compromise, is described. The method corrects for a bias inherent in majority-rule consensus/compromise trees when the source trees exhibit non-independence due to ambiguity in terminal clades. Suggestions are given for its employment in parsimony analyses and tree resampling strategies such as bootstrapping and jackknifing. An R function is described that can be used with the programming language R to produce the consensus.