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Bioinformatics Vol. 18 no. 10 2002
Pages 1297-1304
© 2002 Oxford University Press

SAC 2002 Paper

Optimal algorithms for local vertex quartet cleaning

Gianluca Della Vedova 1,* and H. Todd Wareham 2

1 Dipartimento di Statistica, Universitá degli Studi di Milano–Bicocca, via Bicocca degli Arcimboldi 8, 20126 Milano, Italy
2 Department of Computer Science, Memorial University of Newfoundland, St. John's, NF, Canada A1B 3X5

Received on September 27, 2001 ; accepted on October 24, 2002

Motivation: Reconstructing evolutionary trees is an important problem in biology. A response to the computational intractability of most of the traditional criteria for inferring evolutionary trees has been a focus on new criteria, particularly quartet-based methods that seek to merge trees derived on subsets of four species from a given species-set into a tree for that entire set. Unfortunately, most of these methods are very sensitive to errors in the reconstruction of the trees for individual quartets of species. A recently developed technique called quartet cleaning can alleviate this difficulty in certain cases by using redundant information in the complete set of quartet topologies for a given species-set to correct such errors.

Results: In this paper, we describe two new local vertex quartet cleaning algorithms which have optimal time complexity and error-correction bound, respectively. These are the first known local vertex quartet cleaning algorithms that are optimal with respect to either of these attributes.

Contact: gianluca.dellavedova{at}unimib.it harold{at}cs.mun.ca

* To whom correspondence should be addressed.


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