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Parallelization of MAFFT for large-scale multiple sequence alignments
- Nakamura, Tsukasa, Yamada, Kazunori D, Tomii, Kentaro, Katoh, Kazutaka
- Bioinformatics 2018 v.34 no.14 pp. 2490-2492
- DNA, bioinformatics, computer software, nucleotide sequences, sequence alignment
- 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. This feature is available in MAFFT versions 7.355 or later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary data are available at Bioinformatics online.