An exact algorithm for the geodesic distance between phylogenetic trees

Journal of Computational Biology

Volumn 15, Issue 6, 2008, Pages 577-591

  Kupczok, Anne ^a   Haeseler, Arndt Von ^a,b   Klaere, Steffen ^a  

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

^b MAX F PERUTZ LABORATORIES   (Austria)

Author keywords

Cone path; Geodesic path; Phylogeny; Robinson Foulds distance; Tree space

Indexed keywords

ARTICLE; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; MATHEMATICAL GENETICS; METAZOON; PHYLOGENETIC TREE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; PRIORITY JOURNAL;

ALGORITHMS; PHYLOGENY;

METAZOA;

EID: 47549114831     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0068     Document Type: Article

References (31)

1. Amenta, N., Godwin, M., Postarnakevich, N., et al. 2007. Approximating geodesic tree distance. Inf. Process. Lett. 103, 61-65.
2. Barthélemy, J.-P., and McMorris, F.R. 1986. The median procedure for n-trees. J. Classif. 3, 329-334.
3. Billera, L.J., Holmes, S.P., and Vogtmann, K. 2001. Geometry of the space of phylogenetic trees. Adv. Appl. Math. 27, 733-767.
4. Bridson, M.R., and Haefliger, A. 1999. Metric Spaces of Non-Positive Curvature. Springer, Berlin.
5. Bryant, D. 2003. A classification of consensus methods for phylogenetics. In: Bioconsensus, Janowitz, N.F., Lapointe, F.-J., McMorris, F.R., and Mirkin, B. (eds.). ANS/DIMACS, 2003, 242 pgs.
6. Dutilh, B.E., van Noort, V., van der Heijden, R.T.J.M., et al. 2007. Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23, 815-824.
7. Ebersberger, I. 2007. Human genetic ancestry. Available at: http://www.newton.can.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0907/ ebersberger/. Accessed May 27, 2008.
8. Epstein, D., and Ingram, J. 2003. Computing the BHV metric. Available at: http://www.aimath.org/WWN/geombio/epsteinbhv.pdf. Accessed May 27, 2008.
9. Estabrook, G.F., McMorris, F.R., and Meacham, C.A. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34, 193-200.
10. Ewing, G.B., Ebersberger, I., Schmidt, H.A., et al. 2008. Rooted triple consensus and anomalous gene trees. BMC Evol. Biol. 8, 118.
11. Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
12. Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package), version 3.6. Department of Genome Sciences, University of Washington, Seattle.
13. Gadagkar, S.R., Rosenberg, M.S., and Kumar, S. 2005. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. Exp. Zool. B Mol. Dev. Evol. 304, 64-74.
14. Guindon, S., and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
15. Hein, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98, 185-200.
16. Hillis, D.M., Heath, T.A., and St. John, K. 2005. Analysis and visualization of tree space. Syst. Biol. 54, 471-482.
17. Holmes, S. 2005. Statistical approach to tests involving phylogenies, 91-120. In: Gascuel, O., ed. Mathematics of Evolution and Phylogeny. Oxford University Press, New York.
18. Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468.
19. Notredame, C., Higgins, D., and Heringa, J. 2000. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
20. O'Brien, K.P., Remm, M., and Sonnhammer, E.L.L. 2005. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33, D476-D480.
21. Owen, M. 2007. Computing distances in the space of phylogenetic trees. Preprint. (Cornell University, Ithaca, NY)
22. Pachter, L., and Sturmfels, B. 2007. The mathematics of phylogenomics. SIAM Rev. 49, 3-31.
23. Pattengale, N.D. 2005. Tools for phylogenetic postprocessing [M.A. thesis]. University of New Mexico.
24. Robinson, D.F., and Foulds, L.R. 1978. Comparison of weighted labelled trees. Lect. Notes Math. 748, 119-126.
25. Robinson, D.F., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
26. Rokas, A., and Carroll, S.B. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22, 1337-1344.
27. Smythe, A.B., Sanderson, M.J., and Nadler, S.A. 2006. Nematode small subunit phylogeny correlates with alignment parameters. Syst. Biol. 55, 972-992.
28. Stockham, C., Wang, L.-S., and Warnow, T. 2002. Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics 18, S285-S293.
29. Vogtmann, K. 2003. Geodesics in the space of trees [Technical report]. Cornell University, Ithaca, NY. Available at: http://www.math.cornell.edu/ ~vogtmann/papers/TreeGeodesicss/geodesics07.pdf. Accessed May 27, 2008.
30. Waterman, M.S., and Smith, T.F. 1978. On the similarity of dendrograms. J. Theor. Biol. 73, 789-800.
31. Yule, G.U. 1924. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S. Phil. Trans. R. Soc. Lond. B 213, 21-87.