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.
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