Phylogenetic Parameter Estimation on COWs

Phylogenetic analysis is a routine task in biological research. The growing amounts of biological sequence data makes the computational part a bottleneck of the analysis of these data. Parallel computing is applied to reduce the computational burden. In this chapter we discuss different factors that influences the performance of parallel implementations. Using the example of parameter estimation in the TREEPUZZLE program, we analyze the performance and speedup of different scheduling algorithms on two different kinds of workstation clusters, which are the most abundant parallel platform in biological research. To that end different parts of the TREEPUZZLE program with diverse parallel complexity are examined and the impact of their characteristics are discussed. In addition, an extended parallelization for the parameter estimation program is introduced.

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