Parallelization of the MAFFT multiple sequence alignment program.

ABSTRACT:

Summary

Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. Based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default.

Availability

The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currentl

SUBMITTER: Katoh K 

PROVIDER: S-EPMC2905546 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature