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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).
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Mailund et al. (2004) studied this question.
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