MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function. The input data of MP-EST are rooted binary gene trees produced by the maximum likelihood phylogenetic programs RAxML, PHYML, PHYLIP, and PAUP etc. In addition to the gene tree file, a control file must be generated for running MP-EST. The control file contains necessary parameters for running MP-EST.
citation: Liu, L., L. Yu, S.V. Edwards. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.