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:
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