Prospects for Building the Tree of Life from Large Sequence Databases
Abstract
We assess the phylogenetic potential of ∼300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two “supermatrices” suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.
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This research was supported by the National Science Foundation. Thanks to R. Piaggio and O. Eulenstein for insights on the properties of groves and Wen-Chieh Chang for biclique code. We also thank D. Fernández-Baca and J. Kim.
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Published In
Science
Volume 306 | Issue 5699
12 November 2004
12 November 2004
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American Association for the Advancement of Science.
Submission history
Received: 28 June 2004
Accepted: 14 September 2004
Published in print: 12 November 2004
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www.sciencemag.org/cgi/content/full/306/5699/1172/DC1
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