On the Parallelization of Bioinformatic Applications

This document surveys the computational strategies followed to parallelize the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database searching applications, to very irregularly structured patterns (phylogenetic trees). Fineand coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches, and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed, and shared/distributed memory architectures.