Parallel multiple sequence alignment with dynamic scheduling

This paper proposes a parallel implementation of the multiple sequence alignment algorithm, known as ClustalW, on distributed memory parallel machines. The proposed algorithm divides a progressive alignment into subtasks and schedules them dynamically. A task tree is built according to the dependency of the generated phylogenetic tree. The computation and communication costs of the tasks are estimated at run-time and updated periodically. With dynamic scheduling, tasks are allocated to the processors considering the tasks´ estimated computation and communication costs and the processors´ workload in order to minimize the completion time. The experiment results show that the proposed parallel implementation achieves a considerable speedup over the sequential ClustalW.