Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI
C Objective-C
Latest commit 1cd7716 Feb 14, 2017 @stamatak 1. fixed a bug in quartet checkpointing
2. incremented version number

README.md

ExaML

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI.

This code implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.

When using ExaML please cite the following paper:

Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis: "ExaML Version 3: A Tool for Phylogenomic Analyses on Supercomputers." Bioinformatics (2015) 31 (15): 2577-2579.

It is up to 4 times faster than RAxML-Light [1].

As RAxML-Light, ExaML also implements checkpointing, SSE3, AVX vectorization and memory saving techniques.

[1] A. Stamatakis, A.J. Aberer, C. Goll, S.A. Smith, S.A. Berger, F. Izquierdo-Carrasco: "RAxML-Light: A Tool for computing TeraByte Phylogenies", Bioinformatics 2012; doi: 10.1093/bioinformatics/bts309.

Intel Xeon Phi

For details on running ExaML on Intel MIC (aka Xeon Phi), please refer to README_MIC.txt.