Recursive algorithms for phylogenetic tree counting

Algorithms for Molecular Biology

Volumn 8, Issue 1, 2013, Pages 26-

  Gavryushkina, Alexandra ^a   Welch, David ^a   Drummond, Alexei J ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Bayesian tree prior; Constraint tree; Counting trees; Dynamic algorithms; Phylogenetics; Ranked tree; Resolution

Indexed keywords

EID: 84886120543     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-8-26     Document Type: Article

References (13)

1. Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 1997, 14(7):717-724. 10.1093/oxfordjournals.molbev.a025811, 9214744.
2. Yang Z, Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol 2005, 23:212-226. 10.1093/molbev/msj024, 16177230.
3. Heled J, Drummond A. Tree priors for relaxed phylogenetics and divergence time estimation. Syst Biol 2012, 61:138-149. 10.1093/sysbio/syr087, 3243734, 21856631.
4. Rodrigo AG, Felsenstein J. The Evolution of HIV 1999, Baltimore: Johns Hopkins Univ Press.
5. Drummond A, Pybus O, Rambaut A, Forsberg R, Rodrigo A. Measurably evolving populations. Trends Ecol Evol 2003, 18:481-488.
6. Felsenstein J. Inferring Phylogenies 2004, Sunderland: Sinauer Associates.
7. Murtagh F. Counting dendograms: a survey. Discrete Appl Math 1984, 7:191-199.
8. Gordon AD. A review of hierarchical classification. J R Stat Soc A 1987, 150(2):119-137.
9. Semple C, Steel M. Phylogenetics 2003, New York: Oxford University Press.
10. Griffiths RC. Counting genealogical trees. J Math Biol 1987, 25:423-431. 10.1007/BF00277166, 3668397.
11. Felsenstein J. The number of evolutionary trees. Syst Zool 1978, 23:27-33.
12. Stadler T. Sampling-through-time in birth-death trees. J Theor Biol 2010, 267(3):396-404. 10.1016/j.jtbi.2010.09.010, 20851708.
13. Stadler T, Kouyos RD, von W, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond A, Bonhoeffer S, the Swiss HIV Cohort Study Estimating the basic reproductive number from viral sequence data. Mol Biol Evol 2012, 29:347-357. 10.1093/molbev/msr217, 21890480, the Swiss HIV Cohort Study.