What If I Don't Have a Tree?: Split Decomposition and Related Models
A set of aligned character sequences or a matrix of evolutionary distances often contains a number of different and sometimes conflicting phylogenetic signals, and thus does not always support a unique tree. The method of split decomposition addresses this problem. For ideal data, this method gives rise to a phylogenetic tree, whereas less ideal data are represented by a tree‐like network that may indicate evidence of different and conflicting phylogenies. The SplitsTree program, described here, implements this approach and can be used to compute and visualize phylogenetic networks called splits graphs. It also implements a number of distance transformations, the computation of parsimony splits, spectral analysis and bootstrapping.
Basic Protocol 1: Using SplitsTree Interactively
Alternate Protocol 1: Using the Command‐Line Version of SplitsTree
Figure 6.7.1 Example of an input file in NEXUS format. Usually, an input file will contain either a characters or distances block, but not both.
Figure 6.7.3 The menus provided by SplitsTree.
|Bandelt, H.‐J. and Dress, A.W.M. 1992a. A canonical decomposition theory for metrics on a finite set. Adv. Math. 92:47‐105.|
|Bandelt, H.‐J. and Dress, A.W.M. 1992b. Split decomposition: A new and useful approach to phylogenetic analysis of a distance data. Mol. Phylogenet. Evol. 1:242‐252.|
|Bandelt, H.‐J. and Dress, A.W.M. 1993. A relational approach to split decomposition. In Information and Classification: Concepts, Methods and Applications. (O. Opitz, B. Lausen, and R. Klar, eds.) Heidelberg, Germany.|
|Buneman, P. 1971. The recovery of trees from measures of dissimilarity. In Mathematics and the Archeological and Historical Sciences (F.R. Hodson, D.G. Kendall, and P. Tautu, eds.) pp. 387‐395. Edinburgh University Press, Edinburgh.|
|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|
|Hendy, M.D. and Penny, D. 1993. Spectral analysis of phylogenetic data. J. Classif. 10:5‐24.|
|Huson, D.H. 1998. SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14:68‐73.|
|Jukes, T.H. and Cantor, C.R. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism (H.N. Munro, ed.) p. 21‐132. Academic Press, London.|
|Kimura, M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. U.S.A. 78:454‐458.|
|Lockhart, P.J., Steel, M.A., Hendy, M., and Penny, D. 1994. Recovering the correct tree under a more realistic model of evolution. Mol. Biol. Evol. 11:605‐612.|
|Maddison, D.R., Swofford, D.L., and Maddison, W.P. 1997. NEXUS: An extensible file format for systematic information. Syst. Biol. 46:590‐621.|
|Steel, M.A. 1994. Recovering a tree from the leaf colorations it generates under a markov model. Appl. Math. Lett. 7:19‐24.|
|Bandelt and Dress, 1992a,b, 1993., See above.|
|The theory of split decomposition and related methods was introduced by Hans‐Jürgen Bandelt and Andreas Dress.|
|This Web site contains additional information on SplitsTree, has links to Web servers running the program, and provides downloads of the different versions of the program.|