Distance corrections on recombinant sequences

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

Volumn 2812, Issue , 2003, Pages 271-286

  Bryant, David ^a   Huson, Daniel ^b   Kloepper, Tobias ^b   Nieselt Struwe, Kay ^b  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; COMPUTER SCIENCE; COMPUTERS;

DISTANCE CORRECTIONS; PAIRWISE DISTANCES; PHYLOGENETIC ANALYSIS; SEQUENCE STRUCTURE; STANDARD DISTANCE; TIGHT BOUND;

FORESTRY;

EID: 35248863073     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-39763-2_21     Document Type: Article

References (21)

1. K. Atteson. The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25:251-278, 1999.
2. H.-J. Bandelt and A.W.M. Dress. A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92:47-105, 1992.
3. D. Bryant and V. Moulton. Neighbornet: An agglomerative algorithm for the construction of planar phylogenetic networks. In R. Guigo and D. Gusfield, editors, Workshop in Algorithms for Bioinformatics (WABI), number 2452 in LNCS, pages 375-391. Springer-Verlag, 2002.
4. D. Bryant and V. Moulton. Consistency of the neighbornet algorithm for constructing phylogenetic networks. Technical report, School of Computer Science, McGill University, 2003.
5. J. Chang. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Mathematical Biosciences, 134:189-215, 1996.
6. A.W.M. Dress and D. Huson. Computing phylogenetic networks from split systems (manuscript).
7. O. Gascuel, D. Bryant, and F. Denis. Strengths and limitations of the minimum evolution principle. Systematic Biology, 50:621-627, 2001.
8. R.R. Hudson. Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology, 23:183-201, 1983.
9. T.H. Jukes and C.R. Cantor. Evolution of protein molecules. In H.N. Munro, editor, Mammalian Protein Metabolism, pages 21-123. Academic Press, New York, 1969.
10. M.K. Kuhner and J. Felsenstein. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11:459-168, 1994.
11. M.K. Kuhner, J. Yamato, and J. Felsenstein. Maximum likelihood estimation of recombination rates from population data. Genetics, 156:1393-1401, 2000.
12. J. Maynard-Smith. Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 34:126-129, 1992.
13. D. Posada and K. Crandall. The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution, 54:396-402, 2002.
14. A. Rambaut and N.C. Grassly. Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13:235-238, 1997.
15. F. Rodriguez, J. Oliver, A. Marin, and R. Medina. The general stochastic model of nucleotide substitution. Journal of Theoretical Biology, 142:485-501, 1990.
16. A. Rzhetsky and M. Nei. Theoretical foundation of the minimum evolution method of phylogenetic inference. Molecular Biology and Evolution, 10:1073-1095, 1993.
17. M. Schierup and J. Hein. Consequences of recombination on traditional phylogenetic analysis. Genetics, 156:879-891, 2000.
18. K. Strimmer, C. Wiuf, and V. Moulton. Recombination analysis using directed graphical models. Molecular Biology and Evolution, 18:97-99, 2001.
19. D. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis. Phylogenetic inference. In D.M. Hillis, C. Moritz, and B.K. Mable, editors, Molecular Systematics, pages 407-514. Sinauer, 2nd edition, 1996.
20. K. Tamura and M. Nei. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10:512-526, 1993.
21. C. Wiuf, T. Christensen, and J. Hein. A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution, 18:1929-1939, 2001.