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Parallelization of MAFFT for large-scale multiple sequence alignments.

ABSTRACT: Summary:We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences. Availability and implementation:This feature is available in MAFFT versions 7.355 or later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Nakamura T

PROVIDER: S-EPMC6041967 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Parallelization of MAFFT for large-scale multiple sequence alignments.

Nakamura Tsukasa T Yamada Kazunori D KD Tomii Kentaro K Katoh Kazutaka K

Bioinformatics (Oxford, England) 20180701 14

<h4>Summary</h4>We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 o ...[more]

PMID: 29506019

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