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

  1. Different gene trees may have different outgroups.
  2. The outgroup may have multiple species
  3. The program can optimize the branch lengths for a fixed tree
  4. The program can calculate the log-likelihood score for a fixed tree with branch lengths
  5. The program can optimize the placements of a subset of taxa, while keeping the placements of the remaining taxa fixed.
  6. 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