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  HyPhy Documentation: Standard Analyses: AnalyzeNucDataFreq.bf

      Summary: Given a nucleotide data file, a tree and a nucleotide model, AnalyzeNucDataFreq computes the maximum likelihood estimates for all model parameters and also MLE of the equilibrium frequencies for each of the four nucleotides and reports them to the console.

     Input: A nucleotide data file in any recognizable format. HYPHY uses the following table to translate nucleotide ambiguities. 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 nucleotide models (except for PHYLIP compatible F84) can be selected for the analysis.There are 3 additional parameters introduced by this analysis: estPiA, estPiC and estPiG which stand for the estimated equilibrium frequencies of A,C and G respectively. estPiT is defined as |1-estPiA-estPiC-estPiG|, and represents the equilibrium frequency of T(U). There is also a scaling factor: sum:=estPiA+estPiC+estPiG+estPiT, so the actual frequency estimates are estPiA/sum, etc.

    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. Also, the estimated vector of equilibrium frequencies is displayed.

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

 

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