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MBE Advance Access published online on July 27, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi224
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted July 22, 2005

Research Article

Assessment of Protein Distance Measures and Tree Building Methods for Phylogenetic Tree Reconstruction

Volker Hollich 1*, Lena Milchert 1, Lars Arvestad 2, and Erik L.L. Sonnhammer 1

1 Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, SWEDEN
2 Stockholm Bioinformatics Center, Albanova, Dept of Numerical Analysis and Computer Science, Royal Institute of Technology, 100 44 Stockholm, SWEDEN

* To whom correspondence should be addressed.
Volker Hollich, E-mail: volker.hollich{at}cgb.ki.se


  Abstract

Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining algorithm have been proposed, as well as a number of methods to estimate protein distances. We here present a large-scale assessment of performance in reconstructing the correct tree topology for the most popular algorithms.

The programs BIONJ, FastME, Weighbor, and standard neighbor-joining were run using 12 distance estimators, producing 48 tree building / distance estimation method-combinations. These were evaluated on a test set based on real trees taken from 100 Pfam families. Each tree was used to generate multiple sequence alignments with the ROSE program using three evolutionary models. The accuracy of each method was analyzed as a function of both sequence divergence and location in the tree.

We found that BIONJ produced the overall best results, although the average accuracy differed little between the tree building methods (normally less than a percent). A noticeable trend was that FastME performed poorer than the rest on long branches. Weighbor was several orders of magnitude slower than the other programs.

Larger differences were observed when using different distance estimators. Protein-adapted Jukes-Cantor and Kimura distance correction produced clearly poorer results than the other methods, even worse than uncorrected distances. We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods.

Keywords: Protein distance estimation; Phylogenetic tree reconstruction; Neighbor-joining.
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[Abstract] [Full Text] [PDF]


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