Motivation: To construct a multiple sequence alignment (MSA) of a large number (>∼10 000) of sequences, the calculation of a guide tree with a complexity of O(N2) to O(N3), where N is the number of sequences, is the most time-consuming process.

Results: To overcome this limitation, we have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). The new MSA method with the PartTree algorithm can align ∼60 000 sequences in several minutes on a standard desktop computer. The loss of accuracy in MSA caused by this approximation was estimated to be several percent in benchmark tests using Pfam.

Availability: The present algorithm has been implemented in the MAFFT sequence alignment package ().


Supplementary information: Supplementary information is available at Bioinformatics online.

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