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. MP-EST 2.0 and Manual are now available at Github. New features of Version 2.0 1. It can collapse short internal branches (length<10^-6) of gene trees and treat them as polytomies when calculating triple frequences of gene trees. The input gene trees are still rooted binary trees generated from PHYML or RAxML. MP-EST2.0 can automatically collapse short internal branches. There is no need to use the third-party program to collapse gene trees. 2. It can output a set of triples decomposed from each gene tree. MP-EST 1.6 Manual New features of Version 1.6 Different gene trees may have different outgroups. The outgroup may have multiple species The program can optimize the branch lengths for a fixed tree The program can calculate the log-likelihood score for a fixed tree with branch lengths The program can optimize the placements of a subset of taxa, while keeping the placements of the remaining taxa fixed. Species may have multiple alleles Download (old versions) 1. MP-EST 1.5 Manual 2. MP-EST 1.4 3. MP-EST 1.3 4. MP-EST 1.2 Manual 5. Web server for MP-EST
