title: RAxML-Light: a tool for computing terabyte phylogenies.
abstract: BACKGROUND
  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
  
  
  BACKGROUND
  alexandros.stamatakis@h-its.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-68159 Heidelberg, Germany. alexandros.stamatakis@h-its.org
authors.forename: A
authors.initials: A
authors.lastname: Stamatakis
authors.forename: A J
authors.initials: AJ
authors.lastname: Aberer
authors.forename: C
authors.initials: C
authors.lastname: Goll
authors.forename: S A
authors.initials: SA
authors.lastname: Smith
authors.forename: S A
authors.initials: SA
authors.lastname: Berger
authors.forename: F
authors.initials: F
authors.lastname: Izquierdo-Carrasco
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software