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.
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