Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :) journals.plos.org/ploscompbiol...
Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilitiesAuthor summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...journals.plos.org