An Efficient Program for Phylogenetic Inference Using Simulated Annealing

Authors:
Alexandros Stamatakis
Affiliations:
Foundation for Research and Technology-Hellas, Greece
Venue:
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Year:
2005

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Abstract

Inference of phylogenetic trees comprising thousands of organisms based on the maximum likelihood method is computationally expensive. A new program RAxML-SA (Randomized Axelerated Maximum Likelihood with Simulated Annealing) is presented that combines simulated annealing and hill-climbing techniques to improve the quality of final trees. In addition, to the ability to perform backward steps and potentially escape local maxima provided by simulated annealing, a large number of "good" alternative topologies is generated which can be used to build a consensus tree on the fly. Though, slower than some of the fastest hill-climbing programs such as RAxML-III and PHYML, RAxML-SA finds better trees for large real data alignments containing more than 250 sequences. Furthermore, the performance on 40 simulated 500-taxon alignments is reasonable in comparison to PHYML. Finally, a straight-forward and efficient OpenMP parallelization of RAxML is presented.