Accelerating Parallel Maximum Likelihood-Based Phylogenetic Tree Calculations Using Subtree Equality Vectors

A.P. Stamatakis, T. Ludwig, H. Meier, M.J. Wolf
2002 ACM/IEEE SC 2002 Conference (SC'02)  
Heuristics for calculating phylogenetic trees for a large sets of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. The core of most parallel algorithms, which accounts for the greatest part of computation time, is the tree evaluation function,that calculates the likelihood value for each tree topology. This paper describes and uses Subtree Equality Vectors (SEVs) to reduce the number of required floating point operations during topology evaluation. We
more » ... integrated our optimizations into various sequential programs and into parallel fastDNAml, one of the most common and efficient parallel programs for calculating large phylogenetic trees. Experimental results for our parallel program, which renders exactly the same output as parallel fastDNAml show global run time improvements of 26% to 65%. The optimization scales best on clusters of PCs, which also implies a substantial cost saving factor for the determination of large trees. c 0-7695-1524-X/02 $17.00 (c) 2002 IEEE * This work is partially sponsored under the project ID ParBaum, within the framework of the "Competence Network for Technical, Scientific High Performance Computing in Bavaria": Kompetenznetzwerk für Technisch-Wissenschaftliches Hoch-und Höchstleistungsrechnen in Bayern (KONWIHR). KONWIHR is funded by means of "High-Tech-Offensive Bayern".
doi:10.1109/sc.2002.10016 dblp:conf/sc/StamatakisLMW02 fatcat:yabjw3yrjfcgtata63bb4h44aq