Molecular Biology and Evolution, Vol 11, 459-468, Copyright © 1994 by Society for Molecular Biology and Evolution
MK Kuhner and J Felsenstein
Using simulated data, we compared five methods of phylogenetic tree
estimation: parsimony, compatibility, maximum likelihood, Fitch-
Margoliash, and neighbor joining. For each combination of substitution
rates and sequence length, 100 data sets were generated for each of 50
trees, for a total of 5,000 replications per condition. Accuracy was
measured by two measures of the distance between the true tree and the
estimate of the tree, one measure sensitive to accuracy of branch lengths
and the other not. The distance-matrix methods (Fitch- Margoliash and
neighbor joining) performed best when they were constrained from estimating
negative branch lengths; all comparisons with other methods used this
constraint. Parsimony and compatibility had similar results, with
compatibility generally inferior; Fitch- Margoliash and neighbor joining
had similar results, with neighbor joining generally slightly inferior.
Maximum likelihood was the most successful method overall, although for
short sequences Fitch- Margoliash and neighbor joining were sometimes
better. Bias of the estimates was inferred by measuring whether the
independent estimates of a tree for different data sets were closer to the
true tree than to each other. Parsimony and compatibility had particular
difficulty with inaccuracy and bias when substitution rates varied among
different branches. When rates of evolution varied among different sites,
all methods showed signs of inaccuracy and bias.
ORIGINAL ARTICLE
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates [published erratum appears in Mol Biol Evol 1995 May;12(3):525]
Department of Genetics, University of Washington, Seattle 98195.
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