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Bioinformatics. 2012 Aug 1;28(15):2064-6. doi: 10.1093/bioinformatics/bts309. Epub 2012 May 24.

RAxML-Light: a tool for computing terabyte phylogenies.

Author information

1
The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-68159 Heidelberg, Germany. alexandros.stamatakis@h-its.org

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@h-its.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22628519
PMCID:
PMC3400957
DOI:
10.1093/bioinformatics/bts309
[Indexed for MEDLINE]
Free PMC Article

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