MP-EST (v3.0): Maximum Pseudo-likelihood Estimation of Species Trees

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

MP-EST estimates species trees (topology and branch lengths in coalescent units) from a set of gene trees by maximizing a pseudo-likelihood function. The input data of MP-EST are rooted gene trees. Unlike previous versions, MP-EST3.0 uses the command line interface, i.e., no control file is needed for running MP-EST3.0.

New features in version 3.0

1. MP-EST3.0 can build an NJst tree and use it as the initial tree to find the MP-EST tree.

2. MP-EST3.0 can convert short branches (<1e-06) to polytomies in the gene trees.

3. MP-EST3.0 can take polytomy gene trees as input to estimate species trees.

4. MP-EST3.0 can calculate triplet/quartet distances among gene trees

5. MP-EST3.0 outputs species-tree-gene-tree concordance scores for each internal node of the MP-EST tree.

Installation

There are two ways to install MP-EST:

1. Install from bioconda

MP-EST is available as a package on bioconda. With conda or mamba already installed and your channels set up for bioconda, simply type the following to install:

conda create -n mp-est-env
conda activate mp-est-env
conda install mp-est

This will create a new environment and activate it and then install mp-est from bioconda. Alternateively, you could install in an environment you've already created.

If you use mamba instead of conda, just replace conda with mamba above.

2. Compile from source code

To compile the program from source code, type make and hit return under the directory src.

Usage

Run the program

./mpest -i testgenetree

Help

./mpest -h

Usage: mpest [-i inputfile] [-n #] [-s #] [-u NAME] [-h] [-B|-C|-L|-N|-P|-Q|-T|]
-i: NAME = name of input file in nexus format. Input gene trees must be rooted; polytomy trees are allowed.
-n: # = number of runs [default = 1].
-s: # = seed for random number generator [default = system generated].
-u: NAME = name of user tree file.
-c: # = convert short branches (<#) to polytomies in gene trees.
-h: help message [default = random].
-B: optimize branch lengths of a fixed species tree provided through usertree option -u.
-L: calculate loglikelihood of a species tree provided through usertree option -u.
-N: build NJst tree.
-P: calculate partitions for gene trees.
-Q: calculate pairwise quartet distances among gene trees. Polytomy (unrooted or rooted) gene trees are allowed.
-T: calculate pairwise triple distances of gene trees. Polytomy rooted gene trees are allowed.\

Ouput files

There are two output files; testgenetree_besttree.tre and testgenetree_output.tre. The trees updated in the algorithm are saved in testgenetree_output.tre, while the mpest tree is saved in testgenetree_besttree.tre. If multiple runs are specified in the control file, testgenetree_besttree.tre contains multiple mpest trees.

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.

Old versions

Old versions MP-EST are available at https://github.com/lliu1871/oldversion