AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method

Authors:
Alexandros P. Stamatakis;Thomas Ludwig;Harald Meier;Marty J. Wolf
Affiliations:
-;-;-;-
Venue:
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Year:
2002

Citing 4
Cited 2

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Abstract

Heuristics for the NP-complete problem of calculating the optimal phylogenetic tree for a set of aligned rRNA sequences based on the maximum likelihood method are computationallyexpensive. In most existing algorithms the tree evaluation and branch length optimization functions, calculating the likelihood value for each tree topology examined in the search space, account for the greatest part of overall computation time. This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation function. The algorithmic optimizations introduced, represent a general approach for accelerating thisfunction and are applicable to both sequential and parallel phylogeny programs, irrespective of their search space strategy. Therefore, their integration into three existing phylogeny programs rendered encouraging results. Experimental results on conventional processor architectures show a global run time improvement of 35% up to 47% for the various test sets and program versions we used.