Constructing neighbor-joining phylogenetic trees with reduced redundancy computation

Proceedings of the IEEE International Conference on Electronics, Circuits, and Systems

Volumn , Issue , 2005, Pages

  Chen, Ningtao ^a   Shi, Baochang ^a   Wang, Nengchao ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BOOLEAN FUNCTIONS; JOINING; QUALITY ASSURANCE; REDUNDANCY; RELIABILITY; WINDOWS OPERATING SYSTEM;

BRANCH LENGTHS; COMPACT FORMULAS; CPU TIMES; DISTANCE MATRIXES; FAST ALGORITHMS; LINEAR ARRAYS; NEW ALGORITHMS; OPERATIONAL TAXONOMIC UNITS; PHYLOGENETIC TREES; REDUCED REDUNDANCIES; WINDOWS 2000;

TREES (MATHEMATICS);

EID: 56749157102     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICECS.2005.4633525     Document Type: Conference Paper

References (12)

1. C. Yang and S. Khuri, "PTC: An interactive tool for phylogenetic tree construction," in IEEE Proc. of the Computational Systems Bioinformatics, Stanford University, 2003, 8, pp. 476-477.
2. L. R. Foulds and R. L. Graham, "The steiner problem in phylogeny is NP-complete," Advances Appl. Math. vol. 3, pp. 43-49, 1982.
3. W. Day, "Computational complexity of inferring phylogenies from dissimilarity matrices," Bull. Math. Biol., vol. 49,no. 4,pp. 461-467, 1987.
4. N. Saitou, and M. Nei, "The neighbor-joining method: a new method for reconstructing phylogenetic trees," Mol. Biol. Evol., vol. 4, no. 4, pp. 406-425, 1987.
5. J. Studier and K. Keppler, "A note on the neighbor-joining algorithm of Saitou and Nei," Mol. Biol. Evol. , vol. 5, no. 6, pp. 729-731, 1988.
6. N. Saitou and T. Imanishi, "Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree," Mol. Biol. Evol. , vol. 6, no. 5, pp. 514-525, 1989.
7. J.D. Thompson, D.G. Higgins and T.J. Gibson, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Res. , vol. 22, no. 22, pp. 4673-4680, 1994.
8. C. Notredame, D.G. Higgins and J. Heringa, "T-Coffee: a novel method for fast and accurate multiple sequence alignment," J. Mol. Biol., vol. 302, pp. 205-217, 2000.
9. K. Katoh, K. Misawa, K. Kuma and T. Miyata, "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform," Nucleic Acids Res., vol. 30, no. 14, pp. 3059-3066, 2002.
10. R.C. Edgar, "MUSCLE: multiple sequence alignment with high accuracy and high throughput," Nucleic Acids Res., vol. 32, no. 5, pp. 1792-1797, Mar. 2004.
11. P.H.A. Sneath and R.R. Sokal, Numerical Taxonomy. Freeman, San Francisco, 1973.
12. R.C. Edgar, "Local homology recognition and distance measures in linear time using compressed amino acid alphabets," Nucleic Acids Res., vol. 32, no. 1, pp. 380-385, Jan. 2004.