Optimal algorithms for local vertex quartet cleaning

Bioinformatics

Volumn 18, Issue 10, 2002, Pages 1297-1304

  Della Vedova, Gianluca ^a   Wareham, H Todd ^b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; INFORMATION PROCESSING; MATHEMATICAL GENETICS; MOLECULAR BIOLOGY; PHYLOGENETIC TREE; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SPECIES; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; QUALITY CONTROL; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATISTICAL MODEL;

ALGORITHMS; EVOLUTION, MOLECULAR; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 0036773275     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.10.1297     Document Type: Article

References (12)

1. Ben-Dor,A., Chor,B., Graur,D., Ophir,R. and Pellep,D. (1998) Constructing phylogenies from quartets: elucidation of eutherian superordinal relationships. J. Comput. Biol., 5, 377-390.
2. Berry,V., Bryant,D., Jiang,T., Kearney,P.E., Li,M., Wareham,T. and Zhang,H. (2000) A practical algorithm for recovering the best supported edges of an evolutionary tree. In Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms (SODA2000). pp. 287-296.
3. Berry,V. and Gascuel,O. (2000) Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science, 240, 271-298.
4. Beffy,V., Jiang,T., Kearney,P.E., Li,M. and Wareham,T. (1999) Quartet cleaning: improved algorithms and simulations. In Proceedings of the 7th European Symposium on Algorithm (ESA99). pp. 313-324.
5. Boguski,M. (1998) Bioinformatics-a new era. In Brenner,S., Lewitter,F., Patterson,M. and Handel,M. (eds), Trends Guide to Bioinformatics. Elsevier Science, pp. 1-3.
6. Bryant,D. (1997) Building Trees, Hunting for Trees, and Comparing Trees, PhD thesis, University of Canterbury.
7. Buneman,P. (1971) The recovery of trees from measures of dissimilarity. Mathematics in the Archaelogical and Historical Sciences. Edinburgh University Press.
8. Erdös,P., Steel,M., Székely,L.A. and Warnow,T. (1997) Constructing big trees from short sequences. In Automata, Languages and Programming, 24th International Colloquium (ICALP97), Lecture Notes in Computer Science 1256, pp. 827-837.
9. Hillis,D.M., Moritz,C, and Mable,B.K. (Eds.) (1996) Molecular Systematics, 2nd edn, Sinauer Ass.
10. Jiang,T., Kearney,P. and Li,M. (2000) A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM J. Comput., 30, 1942-1961.
11. Kearney,P. (1998) The ordinal quartet method. In Proceedings of the 2nd Annual International Conference on Computational Molecular Biology (RECOMB98). pp. 125-134.
12. Strimmer,K. and von Haeseler,A. (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13, 964-969.