Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.

Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.

Availability and implementation: The code is available under GNU GPL at https://github.com/sta matak/ExaML.

Contact: Alexandros.Stamatakis@h-its.org

Supplementary information: Supplementary data are available at Bioinformatics online.