RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

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ID: 289131
2006
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Abstract
Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets ≥4000 taxa it also runs 2–3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively. Availability: Contact: Alexandros.Stamatakis@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W2168696662 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Alexandros Stamatakis
Journal BMC Bioinformatics
Year 2006
DOI
10.1093/bioinformatics/btl446
URL
https://doi.org/10.1093/bioinformatics/btl446
Keywords Keywords not found

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