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Bioinformatics Advance Access originally published online on June 16, 2004
Bioinformatics 2004 20(17):3261-3262; doi:10.1093/bioinformatics/bth359
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Applications Note

QuickJoin—fast neighbour-joining tree reconstruction

Thomas Mailund * and Christian N. S. Pedersen

Bioinformatics Research Center (BiRC), University of Aarhus, Høegh-Guldbergs Grade 10, Bldg. 090, DK-8000 Århus C, Denmark

Received on March 5, 2004; revised on May 19, 2004; accepted on June 1, 2004
Advance Access Publication June 16, 2004

Summary: We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm—while still constructing the same tree as the original neighbour-joining algorithm—making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.

Availability: The source code for QuickJoin is available from http://www.birc.dk/Software/QuickJoin under the GNU Public License (GPL).

Contact: mailund{at}birc.dk

* To whom correspondence should be addressed.


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