Molecular Biology and Evolution, Vol 16, 806-816, Copyright © 1999 by Society for Molecular Biology and Evolution
WR Pearson, G Robins and T Zhang
We have developed a phylogenetic tree reconstruction method that detects
and reports multiple topologically distant low-cost solutions. Our method
is a generalization of the neighbor-joining method of Saitou and Nei and
affords a more thorough sampling of the solution space by keeping track of
multiple partial solutions during its execution. The scope of the solution
space sampling is controlled by a pair of user- specified parameters--the
total number of alternate solutions and the number of alternate solutions
that are randomly selected--effecting a smooth trade-off between run time
and solution quality and diversity. This method can discover topologically
distinct low-cost solutions. In tests on biological and synthetic data sets
using either the least- squares distance or minimum-evolution criterion,
the method consistently performed as well as, or better than, both the
neighbor- joining heuristic and the PHYLIP implementation of the
Fitch-Margoliash distance measure. In addition, the method identified
alternative tree topologies with costs within 1% or 2% of the best, but
with topological distances of 9 or more partitions from the best solution
(16 taxa); with 32 taxa, topologies were obtained 17 (least-squares) and 22
(minimum-evolution) partitions from the best topology when 200 partial
solutions were retained. Thus, the method can find lower-cost tree
topologies and near-best tree topologies that are significantly different
from the best topology.
ORIGINAL ARTICLE
Generalized neighbor-joining: more reliable phylogenetic tree reconstruction
Department of Computer Science, University of Virginia, USA. wrp@virginia.edu
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