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.