Trees of trees: An approach to comparing multiple alternative phylogenies

Systematic Biology

Volumn 57, Issue 5, 2008, Pages 785-794

  Nye, Tom M W ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Alternative phylogenies; Consensus tree; Median tree; Parsimony; Split; Topology

Indexed keywords

DNA;

ANIMAL; ARTICLE; CLASSIFICATION; FISH; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PLANT;

ANIMALS; CLASSIFICATION; DNA; EVOLUTION, MOLECULAR; FISHES; GENETIC VARIATION; PHYLOGENY; PLANTS;

ACTINOPTERYGII;

EID: 47249109137     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150802424072     Document Type: Article

References (22)

1. Bandelt, H. 1995. Combination of data in phylogenetic analysis. Plant Syst. Evol. 9:355-361.
2. Bandelt, H., P. Forster, B. Sykes, and M. Richards. 1995. Mitochondrial portraits of human population using median networks. Genetics 141:743-753.
3. Barthélemy, J. 1989. From copair hypergraphs to median graphs with latent vertices. Discrete Math. 76:9-28.
4. Barthélemy, J., and F. McMorris. 1986. The median procedure for n-trees. J. Classif. 3:329-334.
5. Billera, L. and S. Homes. 2001. Geometry of the space of phylogenetic trees. Adv. Appl. Math. 27:733-767.
6. Bonnard, C., V. Berry, and N. Lartillot. 2006. Multipolar consensus for phylogenetic trees. Syst. Biol. 55:837-843.
7. Bryant, D. 2003. A classification of consensus methods for phylogenetics. Pages 163-183 in Bioconsensus. (M. F. Janowitz, F.-J. Lapointe, F. R. Morris, B. Mirkin, and F. S. Roberts, eds.). American Mathematical Society, Providence, RI, USA.
8. Estabrook, G., F. McMorris, and C. Meacham. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34:193-200.
9. Felsenstein, J. 2004. Chapter 30: Consensus trees and distance between trees. Pages 521-538 in Inferring phylogenies. Sinauer, Sunderland, Massachusetts.
10. Hillis, D., T. Heath, and K. St. John. 2005. Analysis and visualization of tree space. Syst. Biol. 54:471-482.
11. Holland, B., K. Huber, V. Moulton, and P. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461.
12. Holland, B., and V. Moulton. 2003. Consensus networks: A method for visualising incompatibilities in collections of trees. Pages 165-176. Springer, in Algorithms in Bioinformatics. (G. Benson and R. Page, eds.). Springer Lecture Notes in Computer Science, Berlin.
13. Huber, K., and V. Moulton. 2005. Phylogenetic networks. Pages 178-204. in Mathematics of phylogeny and evolution (O. Gascuel, ed.). Oxford University Press, Oxford, UK.
14. Huson, D., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
15. Hwang, F., D. Richards, and P. Winter. 1992. The Steiner tree problem. North-Holland, Amsterdam.
16. Li, C., G. Ortí, G. Zhang, and G. Lu. 2007. A practical approach to phylogenetics: The case of ray-finned fish as a case study. BMC Evol. Biol. DOI: 10.1186/1471-2148-7-44
17. Robinson, D. and L. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
18. Rokas, A., B. Williams, N. King, and S. Caroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
19. Sankoff, D. 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28:35-42.
20. Stockham, C., L. Wang, and T. Warnow. 2002. Statistically based post-processing of phylogenetic analysis by clustering. Bioinformatics 18:S285-S293.
21. Swofford, D., G. Olson, P. Wadell, and D. Hillis. 1996. Phylogenetic inference. Pages 411-501 in Molecular systematics (D. Hillis, C. Moritz, and B. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
22. Waterman, M. and T. Smith. 1978. On the similarity of dendrograms. J. Theor. Biol. 73:789-800.