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  HyPhy Documentation: Standard Analyses: AnalyzeCodonData.bf

      Summary: Given a codon data file, a tree and a codon substitution model, AnalyzeCodonData computes the maximum likelihood estimates for all model parameters and reports them to the console.

     Input: A codon data file in any recognizable format. Any of the predefined genetic code translation tables can be used to interpret the data. A Newick style tree string can either be included in the data file, or supplied via a separate tree files. Note, that if a 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 codon 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.

     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