Bioinformatics Advance Access originally published online on August 23, 2006
Bioinformatics 2006 22(21):2688-2690; doi:10.1093/bioinformatics/btl446
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof. Moret, STATION 14, CH-1015 Lausanne, Switzerland
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+
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: icwww.epfl.ch/~stamatak
Contact: Alexandros.Stamatakis{at}epfl.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Received on May 15, 2006; revised on July 21, 2006; accepted on August 16, 2006
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