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Bioinformatics. 2004 Sep 1;20(13):2044-9. Epub 2004 Mar 25.

Phylogenetic trees based on gene content.

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Center for Bioinformatics, Tübingen University, Sand 14, 72076 Tübingen, Germany.


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.


[Indexed for MEDLINE]

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