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 .
As RAxML-Light, ExaML also implements checkpointing, SSE3, AVX vectorization and memory saving techniques.
 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 Xeon Phi, please refer to: