Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts

Journal of Theoretical Biology

Volumn 280, Issue 1, 2011, Pages 159-166

  Holder, Mark T ^a   Steel, Mike ^b  

^a UNIVERSITY OF KANSAS   (United States)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Consistency; Counting processes; Distance based phylogenetic inference; Maximum likelihood; Phylogenetic inference

Indexed keywords

ESTIMATION METHOD; EVOLUTIONARY THEORY; MAXIMUM LIKELIHOOD ANALYSIS; PHYLOGENETICS; TREE;

ACCURACY; ARTICLE; BAYES THEOREM; CALCULATION; CONTROLLED STUDY; GENETIC DISTANCE; INTERMETHOD COMPARISON; INTERNAL CONSISTENCY; MATHEMATICAL MODEL; MAXIMUM LIKELIHOOD METHOD; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; STATISTICAL DISTRIBUTION;

EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 79955498666     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.04.005     Document Type: Article

References (24)

1. Atteson K. The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 1999, 25(2-3):251-278.
2. Barry P. On integer sequences associated with the cyclic and complete graphs. Journal of Integer Sequences 2007, 10. 07.4.8.
3. Beyer W., Stein M., Smith T., Ulam S. A molecular sequence metric and evolutionary trees. Mathematical Biosciences 1974, 19:9-25.
4. Bryant D., Waddell P. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Molecular Biology and Evolution 1998, 15(10):1346-1359.
5. Bulmer M. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Molecular Biology and Evolution 1991, 8(6):868-883.
6. Cavalli-Sforza L., Edwards A. Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 1967, 19(3):233-257.
7. Chang J. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Mathematical Biosciences 1996, 137:51-73.
8. Czarna A., Sanjuán R., González-Candelas F., Wróbel B. Topology testing of phylogenies using least squares methods. BMC Evolutionary Biology 2006, 6(1):105. 10.1186/1471-2148-6-105.
9. Desper R., Gascuel O. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Journal of Computational Biology 2002, 9(5):687-705.
10. Farris, J.S., 1981. Distance data in phylogenetic analysis. In: Funk, V.A., Brooks, D.R. (Eds.), Advances in Cladistics: Proceedings of the First Meeting of the Willi Hennig Society, vol. 1. New York Botanical Garden, Bronx, New York, pp. 3-23.
11. Felsenstein J. Distance methods for inferring phylogenies: a justification. Evolution 1984, 38(1):16-24.
12. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, Massachusetts. first ed.
13. Fitch W., Margoliash E. Construction of phylogenetic trees. Science 1967, 155(3760):279-284.
14. Hasegawa M., Kishino H., Yano T. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 1985, 22:160-174.
15. Lartillot N. Conjugate Gibbs sampling for Bayesian phylogenetic models. Journal of Computational Biology 2006, 13(10):1701-1722. 10.1089/cmb.2006.13.1701.
16. Minin V.N., Suchard M.A. Counting labeled transitions in continuous-time Markov models of evolution. Journal of Mathematical Biology 2008, 56:391-412.
17. Minin V.N., Suchard M.A. Fast, accurate and simulation-free stochastic mapping. Philosophical Transactions of the Royal Society of London, B, Biological Sciences 2008, 363:3985-3995. 10.1098/rstb.2008.0176.
18. Moulton V., Steel M. Retractions of finite distance functions onto tree metrics. Discrete Applied Mathematics 1999, 91:215-233.
19. O'Brein J.D., Minin V., Suchard M. Learning to count: robust estimates for labeled distances between molecular sequences. Molecular Biology and Evolution 2009, 26(4):801-814. 10.1093/molbev/msp003.
20. Roch S. Toward extracting all phylogenetic information from matrices of evolutionary distances. Science 2010, 327(5971):1376-1379. 10.1126/science.1182300.
21. Sanjuan R., Wrobel B. Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures. Systematic Biology 2005, 54(2):218-229. 10.1080/10635150590923308.
22. Susko E. Confidence regions and hypothesis tests for topologies using generalized least squares. Molecular Biology and Evolution 2003, 20(6):862-868. 10.1093/molbev/msg093.
23. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10 2003, Sinauer Associates, Sunderland, Massachusetts.
24. Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Science 2004, 101(30):11030-11035.