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Bioinformatics Advance Access originally published online on March 25, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

Phylogenetic trees based on gene content

Daniel H. Huson 1,* and Mike Steel 2

1 Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany and 2 Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand

Received on September 10, 2003; revised on December 19, 2003; accepted on January 14, 2004
Advance Access Publication March 25, 2004

Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known ‘fact’ that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method.

Availability: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html

Contact: huson{at}informatik.uni-tuebingen.de

* To whom correspondence should be addressed.


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