Journal
BIOINFORMATICS
Volume 26, Issue 15, Pages 1899-1900Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq224
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Funding
- KAKENHI, Monbukagakusho, Japan [21700326]
- Grants-in-Aid for Scientific Research [21700326] Funding Source: KAKEN
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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.
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