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 computationally expensive. 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 the overall computation time. This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation junction. The algorithmic optimizations introduced, represent a general approach for accelerating this function 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

@inproceedings{AAFPFSAPPT02,
	author	 = {Alexandros P. Stamatakis and Thomas Ludwig and Harald Meier and Marty J. Wolf},
	title	 = {{AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method}},
	year	 = {2002},
	booktitle	 = {{Proceedings of 1. IEEE Bioinformatics Conference}},
	publisher	 = {IEEE Computer Society},
	address	 = {Washington, DC, USA},
	pages	 = {21--28},
	conference	 = {CSB-02},
	organization	 = {Stanford University},
	location	 = {Palo Alto, California, USA},
	isbn	 = {0-7695-1653-X},
	doi	 = {http://dx.doi.org/10.1109/CSB.2002.1039325},
	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 computationally expensive. 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 the overall computation time. This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation junction. The algorithmic optimizations introduced, represent a general approach for accelerating this function 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},
}