articleBioinformaticsApr 28, 2010HYBRID OA

Parallelization of the MAFFT multiple sequence alignment program

KKKazutaka KatohHTHiroyuki Toh

National Institute of Advanced Industrial Science and Technology

PubMed
Indexed incrossrefdoajpubmed

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…

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954
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Authors

2

Topics & keywords

Topics
Keywords
  • Computer science
  • POSIX Threads
  • Benchmark (surveying)
  • Multiple sequence alignment
  • Parallel computing
  • Sequence (biology)
  • Software
  • POSIX
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