The geometry of the neighbor-joining algorithm for small trees

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5147 LNCS, Issue , 2008, Pages 81-95

  Eickmeyer, Kord ^a   Yoshida, Ruriko ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BOOLEAN ALGEBRA; CONFORMAL MAPPING; EVOLUTIONARY ALGORITHMS; JOINING; MAPS; MATRIX ALGEBRA; OPTICAL PROJECTORS;

COMBINATORICS; INTERNATIONAL CONFERENCES; MINIMUM EVOLUTION; NEIGHBOR-JOINING; PHYLOGENETIC RECONSTRUCTION; SMALL PERTURBATIONS; SMALL TREES; TREE METRICS; TREE MODELS;

TREES (MATHEMATICS);

EID: 52949108511     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-85101-1_7     Document Type: Conference Paper

References (19)

1. Atteson, K.: The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25, 251-278 (1999)
2. Bryant, D.: On the uniqueness of the selection criterion in neighbor-joining. J. Classif. 22, 3-15 (2005)
3. Eickmeyer, K., Huggins, P., Pachter, L., Yoshida, R.: On the optimality of the neighbor-joining algorithm. Algorithms in Molecular Biology 3 (2008)
4. Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17, 368-376 (1981)
5. Galtier, N., Gascuel, O., Jean-Marie, A.: Markov models in molecular evolution. In: Nielsen, R, (ed.) Statistical Methods in Molecular Evolution, pp. 3-24 (2005)
6. Gawrilow, E., Joswig, M.: Polymake: a framework for analyzing convex polytopes. In: Kalai, G., Ziegler, G.M. (eds.) Polytopes -Combinatorics and Computation, pp. 43-74 (2000)
7. Kimura, M.: A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111-120 (1980)
8. Neyman, J.: Molecular studies of evolution: a source of novel statistical problems. In: Gupta, S., Yackel, J. (eds.) Statistical decision theory and related topics, pp. 1-27. New York Academic Press, London (1971)
9. Jukes, H.T., Cantor, C.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, pp. 21-32. New York Academic Press, London (1969)
10. Levy, D., Yoshida, R., Pachter, L.: Neighbor-joining with phylogenetic diversity estimates. Molecular Biology and Evolution 23, 491-498 (2006)
11. Mihaescu, R., Levy, D., Pachter, L.: Why Neighbor-Joining Works. Algorithmica (2008)
12. Olsen, G.J., Matsuda, H., Hagstrom, R., Overbeek, R.: fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput, Appl. Biosci. 10, 41-48 (1994)
13. Ota, S., Li, W.H.: NJML: A Hybrid algorithm for the neighbor-joining and maximum likelihood methods. Molecular Biology and Evolution 17(9), 1401-1409 (2000)
14. Saitou, N., Nei, M.: The neighbor joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425 (1987)
15. Gascuel, O., Steel, M.: Neighbor-joining revealed. Molecular Biology and Evolution 23, 1997-2000 (2006)
16. Studier, J.A., Keppler, K.J.: A note on the neighbor-joining method of Saitou and Nei. Molecular Biology and Evolution 5, 729-731 (1988)
17. Yang, Z.: PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 15, 555-556 (1997)
18. Yang, Z.: Complexity of the simplest phylogenetic estimation problem. Proceedings of the Royal Society B: Biological Sciences 267, 109-116 (2000)
19. Ziegler, G.: Lectures on Polytopes. Springer, Heidelberg (1995)