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.
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)
2. MP-EST 1.4
3. MP-EST 1.3