Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method |
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Authors: | Jason Evans Luke Sheneman James Foster |
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Institution: | (1) Department of Biological Sciences, University of Idaho, P.O. Box 443051, Moscow, ID 83844-3051, USA |
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Abstract: | Our ability to construct very large phylogenetic trees is becoming more important as vast amounts of sequence data are becoming
readily available. Neighbor joining (NJ) is a widely used distance-based phylogenetic tree construction method that has historically
been considered fast, but it is prohibitively slow for building trees from increasingly large datasets. We developed a fast
variant of NJ called relaxed neighbor joining (RNJ) and performed experiments to measure the speed improvement over NJ. Since
repeated runs of the RNJ algorithm generate a superset of the trees that repeated NJ runs generate, we also assessed tree
quality. RNJ is dramatically faster than NJ, and the quality of resulting trees is very similar for the two algorithms. The
results indicate that RNJ is a reasonable alternative to NJ and that it is especially well suited for uses that involve large
numbers of taxa or highly repetitive procedures such as bootstrapping.
Reviewing Editor: Dr. James Bull] |
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Keywords: | Phylogenetic tree construction Neighbor joining Distance method |
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