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

被引:13793
作者
Stamatakis, Alexandros [1 ]
机构
[1] Swiss Fed Inst Technol, Sch Comp & Commun Sci, Lab Prof Moret, CH-1015 Lausanne, Switzerland
关键词
D O I
10.1093/bioinformatics/btl446
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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+Gamma 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.
引用
收藏
页码:2688 / 2690
页数:3
相关论文
共 11 条
[11]  
Stamatakis A., 2006, P IPDPS2006 RHOD GRE