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  HyPhy Documentation: Standard Analyses: StarDecomposition.bf

      Summary: Given a nucleotide, aminoacid or codon data file and a relevant model, StarDecomposition heuristically reconstructs a phylogenetic tree for the sequences in the data using the method of star decomposition with maximum likelihood criterion.

For a description of the method refer to:

        Molecular Systematics, by David M. Hillis (Editor), Craig Moritz (Editor), Barbara K. Mable (Editor)         2nd edition (January 1996) Sinauer Assoc; ISBN: 0878932828 , pg. 483-484.

     Input: A nucleotide, aminoacid or codon data file in any recognizable format. HYPHY uses the following table to translate nucleotide ambiguities (or aminoacid characters). For codon files, any of the predefined genetic code translation tables can be used to interpret the data.

    The user will be prompted to choose a branch swapping method for the tree reconstruction analysis.

  • No swapping: No branch swapping is performed.
  • Global NNI: Greedy NNI is performed on the final tree. The number of additional trees examined is proportional to the number of sequences.
  • Global SPR: SPR is performed on the final tree. The number of additional trees examined is proportional to the square of the number of sequences.

    Models: Any of the standard nucleotide , aminoacid or codon models can be selected for the analysis. The selected model will be applied to estimate the maximum likelihood parameter values, and the likelihood of the tree being tested.

    Output: The standard output depends on the "Likelihood Output" option selected in "Preferences". By default, that option is to print the maximum ln-likelihood followed by a the inferred tree string with branch lengths representing the expected number of substitutions per codon. For a complete list of output options, refer the Output Formats page. Also, the estimated vector of equilibrium frequencies is displayed. The inferred tree topology can be optionally saved to a file.

     Result Processing Tools: After the analysis is finished, the following options are available in the "Results" submenu of the "Analyses" menu:

  • View Results.
  • Save Results.
  • (Co)Variance Estimates.
    The (co)variance estimates refer to the parameters in the inferred tree.
  • Nonparametric Bootstrap.
  • Given a number of iterations, for each iteration: resample (with replacement) the original sequence data, reconstruct the phylogeny for the simulated data set, write out the tree string to the user-specified output file; also each simulated tree is checked against the tree yielded by the original data, and all the clades present in both trees are noted. At the end of the run, a summary tree is printed; this tree has the same topology as the tree reconstructed from the original data, and internal branch lengths represent the proporion (or raw count) of simulated trees which contained the clade starting at that internal node.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002