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PubMed · 15878123

Identifying optimal incomplete phylogenetic data sets from sequence databases.

Changhui Yan·J Gordon Burleigh·Oliver Eulenstein
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Abstract

We introduce a new method for identifying optimal incomplete data sets from large sequence databases based on the graph theoretic concept of alpha-quasi-bicliques. The quasi-biclique method searches large sequence databases to identify useful phylogenetic data sets with a specified amount of missing data while maintaining the necessary amount of overlap among genes and taxa. The utility of the quasi-biclique method is demonstrated on large simulated sequence databases and on a data set of green plant sequences from GenBank. The quasi-biclique method greatly increases the taxon and gene sampling in the data sets while adding only a limited amount of missing data. Furthermore, under the conditions of the simulation, data sets with a limited amount of missing data often produce topologies nearly as accurate as those built from complete data sets. The quasi-biclique method will be an effective tool for exploiting sequence databases for phylogenetic information and also may help identify critical sequences needed to build large phylogenetic data sets.

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Base SequenceClassificationComputational BiologyComputer SimulationData Interpretation, StatisticalPhylogenyComparative StudyJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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Changhui Yan, J Gordon Burleigh, Oliver Eulenstein. 2005-03-21. Identifying optimal incomplete phylogenetic data sets from sequence databases.. https://doi.org/10.1016/j.ympev.2005.02.008

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