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Bioinformatics Advance Access originally published online on April 1, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

A weighted least-squares approach for inferring phylogenies from incomplete distance matrices

Vladimir Makarenkov 1,2,* and François-Joseph Lapointe 3

1 Département d'Informatique, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec, Canada H3C 3P8, 2 Institute of Control Sciences, 65 Profsoyuznaya, Moscow 117806, Russia and 3 Département de Sciences Biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7

Received on April 4, 2003; revised on February 20, 2004; accepted on February 20, 2004
Advance Access Publication April 1, 2004

Motivation: The problem of phylogenetic inference from datasets including incomplete or uncertain entries is among the most relevant issues in systematic biology. In this paper, we propose a new method for reconstructing phylogenetic trees from partial distance matrices. The new method combines the usage of the four-point condition and the ultrametric inequality with a weighted least-squares approximation to solve the problem of missing entries. It can be applied to infer phylogenies from evolutionary data including some missing or uncertain information, for instance, when observed nucleotide or protein sequences contain gaps or missing entries.

Results: In a number of simulations involving incomplete datasets, the proposed method outperformed the well-known Ultrametric and Additive procedures. Generally, the new method also outperformed all the other competing approaches including Triangle and Fitch which is the most popular least-squares method for reconstructing phylogenies. We illustrate the usefulness of the introduced method by analyzing two well-known phylogenies derived from complete mammalian mtDNA sequences. Some interesting theoretical results concerning the NP-hardness of the ordinary and weighted least-squares fitting of a phylogenetic tree to a partial distance matrix are also established.

Availability: The T-Rex package including this method is freely available for download at http://www.info.uqam.ca/~makarenv/trex.html

Contact: makarenkov.vladimir{at}uqam.ca

* To whom correspondence should be addressed.


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