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Bioinformatics Advance Access originally published online on November 21, 2006
Bioinformatics 2007 23(3):372-374; doi:10.1093/bioinformatics/btl592
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.


  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 be several percent in benchmark tests using Pfam.

Availability: The present algorithm has been implemented in the MAFFT sequence alignment package (http://align.bmr.kyushu-u.ac.jp/mafft/software/).

Contact: katoh{at}bioreg.kyushu-u.ac.jp

Supplementary information: Supplementary information is available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on August 23, 2006; revised on October 30, 2006; accepted on November 17, 2006

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Home page
 Brief BioinformHome page
K. Katoh and H. Toh
Recent developments in the MAFFT multiple sequence alignment program
Brief Bioinform, July 1, 2008; 9(4): 286 - 298.
[Abstract] [Full Text] [PDF]


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