Bioinformatics Vol. 17 no. 9 2001
Pages 821-828
© 2001 Oxford University Press
A simple algorithm to infer gene duplication and speciation events on a gene tree
Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
Received on January 24, 2001
; revised on April 5, 2001
; accepted on April 6, 2001
Motivation: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein’s function than paralogous sequences (that diverged by gene duplication), because duplication enables functional diversification. The utility of phylogenetic information in high-throughput genome annotation (‘phylogenomics’) is widely recognized, but existing approaches are either manual or indirect (e.g. not based on phylogenetic trees). Our goal is to automate phylogenomics using explicit phylogenetic inference. A necessary component is an algorithm to infer speciation and duplication events in a given gene tree.
Results: We give an algorithm to infer speciation and duplication
events on a gene tree by comparison to a trusted species tree. This
algorithm has a worst-case running time of O(
)
which is inferior to two previous algorithms that are
O(
) for a gene tree of sequences.
However, our algorithm is extremely simple, and its asymptotic worst
case behavior is only realized on pathological data sets. We show
empirically, using 1750 gene trees constructed from the Pfam protein
family database, that it appears to be a practical (and often
superior) algorithm for analyzing real gene trees.
Availability: http://www.genetics.wustl.edu/eddy/forester
Contact: zmasek{at}genetics.wustl.edu; eddy{at}genetics.wustl.edu
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