Bi-de: An application for simulating phylogenetic processes

Bioinformatics

Volumn 12, Issue 6, 1996, Pages 469-471

  Rambaut, Andrew ^a   Grassly, Nicholas C ^a   Nee, Sean ^a   Harvey, Paul H ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIRTH RATE; COMPUTER PROGRAM; COMPUTER SIMULATION; EVOLUTION; MOLECULAR GENETICS; MORTALITY; PHYLOGENY; POPULATION; PRIORITY JOURNAL; TIME;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; DEATH; EVOLUTION, MOLECULAR; FEMALE; HUMANS; LABOR, OBSTETRIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PREGNANCY; SOFTWARE;

EID: 0030463094     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.6.469     Document Type: Article

References (27)

1. Adell, J.C. and Dopazo, J. (1994) Monte Carlo simulation in phytogenies: An application to test the constancy of evolutionary rates. J. MoL Evoi, 38, 305-309.
2. Atchley.W.R. and Fitch, W.M. (1991) Gene trees and the origins of inbred strains of mice. Science, 254, 554-558.
3. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
4. Felsenstein, J. (1995) PHYUP. University of Washington, Seattle.
5. Garland, TJ., Dickennan, A.W., Janis, C.M. and Jones, J.A. (1993) Phylogenetic analysis of covariance by computer simulation. Sysl. BioL, 42, 265-292.
6. Gaut.B.S. and Lewis.P.O. (1995) Success of maximum likelihood phylogeny inference in the four-taxon case. MoL BioL EvoL, 12, 152-162.
7. Harpending, H.C, Sherry.S.T., RogersAR-and Stonelring.M. (1993) The genetic structure of ancient human populations. Curr. Anthrop., 34, 483— 496.
8. Harvey.P.H. and Nee, S. (1993) New uses for new phylogenies. Eur. Rev., 1, 11-19.
9. Harvey, H., Holmes, E.G, Mooers, A. and Nee, S. (1994a) In Scotland, R.W., Siebert, DJ. and Williams, D.M. (eds), Inferring Evolutionary Processes from Molecular Phylogenies. Systematics Association Special Volume Series, London, Vol. 52, pp. 313-333.
10. Harvey, P.H., May, R.M. and Nee, S. (1994b) Phylogenies without fossils: estimating lineage birth and death rates. Evolution, 48, 523-529.
11. Hasegawa.M., Kishino.H. and Yano, T. (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. EvoL, 22, 160-174.
12. Heard.S.B. (1992) Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution, 46, 1818-1826.
13. Hillis, D.M. (1995) Approaches for assessing phylogenetic accuracy. Syst. BioL, 44, 3-16.
14. Hillis, D.M., Bul, U.J., White, M.E., Badgett, M.R. and Molineux, I.J. (1992) Experimental phylogenetics: Generation of a known phylogeny. Science, 255, 589-592.
15. Holmes, C, Nee, S., Rambaut, A, Garnet, G.P. and Harvey, P.H. (1995) Revealing the history of infectious disease epidemics through phylogenetic trees. Philos. Trans. R.. Soc. Ser. B, 349, 33-40.
16. Hudson, R.R. (1990) Gene genealogies and the coalescent process. Oxf. Surv. Evol. BioL, 7, 1-44.
17. HuelsenbeckJ.P. (1995) Performance of phylogenetic methods in simulation. Syst. BioL, 44, 17-48.
18. Jukes, T.H. and Cantor, C.R. (1969) In Munro, H.N. (ed.), Evolution of Protein Molecules. Academic Press, New York, pp. 21-123.
19. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. MoL EvoL, 16, 111-120.
20. Kuhner, M.K. and Felsenstein, I. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. BioL EvoL, 11, 459-468.
21. Nee, S., Holmes, E.C, May, R.M. and Harvey, P.H. (1994a) In LawtonJ.L. and May.R.M. (eds), Estimating Extinction from Molecular Phylogenies. Oxford University Press, Oxford, pp. 164-182.
22. Nee.S., Holmes, E.C, May, R.M. and Harvey, P.H. (1994b) Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R.. Soc. Ser. B, 344, 77-82.
23. Nee, S., Holmes, E.C., Rambaut, A and Harvey, P.H. (1995) Inferring population history from molecular phylogenies. Philos. Trans. R.. Soc. Ser. B, 349, 25-31.
24. Nce, S., MooersA-and Harvey, P.H. (1992) The tempo and mode of evolution revealed from molecular phylogenies. Proc Natl Acad. Sci. USA, 89, 8322-8326.
25. Purvis, A, Nee, S. and Harvey, P.H. (1995) Macroevolutionary inferences from primate phylogeny. Proc. R. Soc. London Ser. B, 260, 329-333.
26. Raup.D.M., Gould, SJ., Schopf.TJ.M. and Simberloff, D.S. (1973) Stochastic models of phylogeny and the evolution of diversity. J. GeoL, 81, 525-542.
27. Slatkin.M. and Hudson, R.R. (1991) Pairwise comparison of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.