Summary:
Given a nucleotide, aminoacid or codon data file and a relevant
model, StarDecomposition heuristically reconstructs a phylogenetic
tree for the sequences in the data using the method of star decomposition
with maximum likelihood criterion.
For a description of the method refer to:
Molecular
Systematics, by David M. Hillis (Editor), Craig Moritz
(Editor), Barbara K. Mable (Editor) 2nd
edition (January 1996) Sinauer Assoc; ISBN: 0878932828 , pg.
483-484.
Input:
A nucleotide, aminoacid or codon data file in any recognizable format. HYPHY
uses the following table
to translate nucleotide ambiguities (or aminoacid
characters). For codon files, any of the predefined
genetic code translation tables can be used to interpret
the data.
The user will be prompted to choose
a branch swapping method for the tree reconstruction analysis.
- No swapping: No branch swapping is performed.
- Global NNI: Greedy NNI is performed
on the final tree. The number
of additional trees examined is proportional to the number of
sequences.
- Global SPR: SPR is performed
on the final tree. The number
of additional trees examined is proportional to the square of the number of
sequences.
Models: Any of the standard
nucleotide , aminoacid
or codon models can
be selected for the analysis. The selected model will be applied
to estimate the maximum likelihood parameter values, and the
likelihood of the tree being tested.
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 the inferred 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. The inferred tree topology can be optionally saved
to a file.
Result
Processing Tools: After the analysis is finished, the
following options are available in the "Results" submenu of the "Analyses" menu:
- View Results.
- Save Results.
- (Co)Variance Estimates.
The (co)variance
estimates refer to the parameters in the inferred tree.
- Nonparametric Bootstrap.
Given a number of iterations,
for each iteration: resample (with replacement) the original
sequence data, reconstruct the phylogeny for the simulated data set, write out
the tree string to the user-specified output file; also each simulated tree is checked
against the tree yielded by the original data, and all the clades present in both
trees are noted. At the end of the run, a summary tree is printed; this tree has
the same topology as the tree reconstructed from the original data, and internal
branch lengths represent the proporion (or raw count) of simulated trees which
contained the clade starting at that internal node.
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