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Bioinformatics Vol. 19 no. 11 2003
Pages 1412-1416
© 2003 Oxford University Press

GeneTRACE–reconstruction of gene content of ancestral species

Victor Kunin and Christos A. Ouzounis *

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK

Received on November 11, 2002 ; revised on January 22, 2003 ; accepted on February 20, 2003

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.

Contact: ouzounis{at}ebi.ac.uk

* To whom correspondence should be addressed.


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