RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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DOI：
10.1093/bioinformatics/btl446
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发表时间：
2006-11-01
期刊：
影响因子：
5.8
通讯作者：
Stamatakis, Alexandros
中科院分区：
文献类型：
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作者：
Stamatakis, Alexandros
RAxML-VI-HPC（randomized axelerated maximum likelihood for high performance computing）是一个串行和并行程序，用于用最大似然（ML）推理大的概率。低层次的技术优化，搜索算法的修改，以及使用GTR+CAT近似作为GTR+Gamma的替代，产生了比以前版本的RAxML快2.7到52倍的程序。一个大规模的性能比较与GARLI，PHYML，IQPNNI和MrBayes的真实的数据包含1000至6722分类表明，RAxML需要至少5.6倍的主内存，并产生更好的树在类似的时间比最好的竞争程序（GARLI）的数据集高达2500个分类。在数据集>= 4000 taxa它也运行2-3倍的速度比GARLI。RAxML已经与MPI并行化，可以在不同的起始树上进行并行的多个引导和推理。该程序已被用来计算ML树上的两个最大的比对，到目前为止，包含25 057（1463 bp）和2182（51 089 bp）分类群，分别。
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.