RAxML-Light: a tool for computing terabyte phylogenies

• Published in: Bioinformatics 2012-08, Vol.28 (15), p.2064-2066
• Main Authors: STAMATAKIS, A, ABERER, A. J, GOLL, C, SMITH, S. A, BERGER, S. A, IZQUIERDO-CARRASCO, F
• Format: Article
• Language: English
• Subjects: Applications Note; Biological and medical sciences; Computational Biology - methods; Computer Simulation; Fundamental and applied biological sciences. Psychology; General aspects; Likelihood Functions; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Phylogeny; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts309

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. 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 [e-mail] Supplementary data are available at Bioinformatics online.