RAxML-Light: a tool for computing terabyte phylogenies

Abstract

Motivation: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores.

Results: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree.

Code Availability: https://github.com/stamatak/RAxML-Light-1.0.5

Data Availability: http://www.exelixis-lab.org/onLineMaterial.tar.bz2

Contact: alexandros.stamatakis@ 123456h-its.org

Supplementary Information: Supplementary data are available at Bioinformatics online.