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Bioinformatics Advance Access published online on November 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl592
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© 2006 The Author(s)
Received August 23, 2006
Revised October 30, 2006
Accepted November 17, 2006

Applications note

PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences

Kazutaka Katoh 1 * and Hiroyuki Toh 2

1 Digital Medicine Initiative, Kyushu University, Fukuoka 812-8582, Japan
2 Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan

* To whom correspondence should be addressed.
Kazutaka Katoh, E-mail: katoh{at}bioreg.kyushu-u.ac.jp


  Abstract

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 several percent in benchmark tests using Pfam.

Availability: The present algorithm has been implemented in the MAFFT sequence alignment package. http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/.

Associate Editor: Thomas Lengauer
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