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  HyPhy Documentation: Standard Analyses: AnalyzeNucProtData.bf

      Summary: Given a nucleotide (or aminoacid) data file, a tree and a nucleotide (or aminoacid) model, AnalyzeNucProtData computes the maximum likelihood estimates for all model parameters and reports them to the console.

     Input: A nucleotide (or aminoacid) data file in any recognizable format. HYPHY uses the following table to translate nucleotide ambiguities (or aminoacid characters). A Newick style tree string can either be included in the data file, or supplied via a separate tree file. Note, that if the data file contains more than one tree, only the first one will be read.
    Note that HyPhy may reroot the tree to speed up likelihood calculations.

    Models: Any of the standard nucleotide (or aminoacid) models can be selected for the analysis.

    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 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.
    For GUI versions of HyPhy, a graphical tree panel with may appear after the analysis has finished (that is controlled via Preferences).

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

        Bootstrapping tools output a summary of simulations on the screen (sample mean and variance for each independent parameter) and save detailed MLE of each data replicate in a comma-separated file suitable for import by data processing programs.

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