SplitsTree: Analyzing and visualizing evolutionary data

Bioinformatics

Volumn 14, Issue 1, 1998, Pages 68-73

  Huson, Daniel H ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; EVOLUTION; HUMAN; INTERNET; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SPECTROSCOPY;

EID: 0031678692     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.1.68     Document Type: Article

References (30)

1. Adachi, J. and Hasegawa, M. (1995) Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among ammo acid sites. J. Mol. Evol., 40, 622-628.
2. Bandelt, H.-J. and Dress, A.W.M. (1992a) A canonical decomposition theory for metrics on a finite set. Adv. Math., 92, 47-05.
3. Bandelt, H.-J. and Dress, A.W.M. (1992b) Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol., 1, 242-252.
4. Bandelt, H.-J. and Dress, A.W.M. (1993) A relational approach to split decomposition. In Opitz, O., Lausen, B. and Klar, R. (eds), Information and Classification. Springer, Berlin, pp. 123-131.
5. Buneman, P. (1971) The recovery of trees from measures of dissimilarity. In Mathematics and the Archeological and Historical Sciences. Edinburgh University Press, pp. 387-395.
6. Dayhoff, M.O., Barker, W.C. and Hunt, L.T. (1983) Establishing homologies in protein sequences. Methods Enzymol, 91, 524-545.
7. Delwiche, C.F., Kushel, M. and Palmer, J.D. (1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogenet. Evol., 4, 110-128.
8. Dopazo, J., Dress, A.W.M. and von Haeseler, A. (1993) Split decomposition: a new technique to analyse viral evolution. Proc. Natl Acad. Sci. USA, 90, 10320-10324.
9. Dress, A.W.M. and Wetzel, R. (1993) The human organism - a place to thrive for the immuno-deficiency virus. In Proceedings of IFCS. Paris.
10. Dress, A.W.M., Huson, D.H and Moulton, V. (1996) Analyzing and visualizing sequence and distance data using splitstree. Discrete Appl. Math., 71, 95-109.
11. Felsenstein, J. (1985) Confidence limits on phytogenies: an approach using the bootstrap. Evolution, 39, 783-791.
12. Fitch, W. (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20, 406-416.
13. Hendy, M.D. and Penny, D. (1992) Spectral analysis of phylogenetic data. J Classif., 10, 5-24.
14. Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In Munro, H.N. (ed.), Mammalian Protein Metabolism. Academic Press, New York, pp. 21-132.
15. Kimura, M. (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl Acad. Sci. USA, 78, 454-458.
16. Lockhart, P.J., Steel, M.A., Hendy, M.D. and Penny, D.P. (1994) Recovering an evolutionary tree under a more realistic model of sequence evolution. Mol. Biol. Evol., 11, 605-612.
17. Lockhart, P.J., Penny, D. and Meyer, A. (1995) Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis. Mol. Evol., 41, 666-674.
18. Lockhart, P.J., Larkum, A.W.D., Steel, M.A., Waddell, P.J. and Penny, D. (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad. Sci USA, 93, 1930-1934
19. Maddison, W.P and Maddison, D.R. (1989) Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol., 53, 190-202.
20. Maddison, D.R., Swofford, D.L. and Maddison, W.P. (1995) NEXUS: An extendible file format for systematic information. Syst. Biol., in press.
21. McLenachan, P.A., Lockhart, P.J., Faber, H.R. and Mansfield, B.C. (1996) Evolutionary analysis of the multigene pregnancy specific β1-glycoprotein family: separation of historical and non historical signals. J. Mol. Evol., 42, 273-280.
22. Moulton, V., Steel, M.A. and Tuffley, C. (1997) Dissimilarity maps and substitution models: some new results. Proceedings of the DIMACS Workshop on Mathematical Hierarchies and Biology. American Mathematical Society, in press.
23. Nei, M. and Miller, J.C. (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics, 1256, 873-879.
24. Sidow, A., Nguyen, T. and Speed, T.P. (1992) Estimating the fraction of invariable codons with a capture-recapture method. J. Mol. Evol., 35, 253-260.
25. Swofford, D.L. (1997) PAUP 5.0. Sinaur Associates, Sunderland, MA.
26. Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M (1996) Phylogenetic inference. In Hillis, D.M., Moritz, C. and Mable, B.K. (eds), Molecular Systematics, 2nd edn. Sinauer Associates, Sunderland, MA, pp. 407-514.
27. Steel, M.A. (1994) Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett., 7, 19-24.
28. Van de Peer, Y., Rensing, S.A., Maier, U.G and De Wachter, R. (1996) Substitution rate calibration of small ribosomal subunit RNA identifies chlorachniophyte endosymbionts as remnants of green algae. Proc. Natl Acad. Sci. USA, 93, 7732-7736.
29. Waddell, P.J. (1996) Statistical methods of phylogenetic analysis, including Hadamard conjugations, LogDet transforms, and maximum likelihood. PhD Thesis, Massey University, New Zealand.
30. Wetzel, R. (1995) Zur Visualisierung abstrakter Ähnlichkeitsbeziehungen. PhD Thesis, University of Bielefeld.