prime-phylo

bayesian estimation of gene trees taking the species tree into account

PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.