Summary:
Given a nucleotide, aminoacid or codon data file, a tree and a
substiution model, BranchSwap performs branch swapping using the method
of Nearest Neighbor Interchange (NNI)
in an attempt to improve the likelihood of the tree.
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.
A starting tree is also needed. It may either be present
in the data file, or reside in a separate (Newick string) file.
The user will be given two swapping strategies to choose from:
-
Greedy: as soon as a better likelihood tree is found, the
NNI procedure is restarted on that tree. The procedure repeats
until no further likelihood improvements can be obtained.
This strategy tends to be faster.
-
Patient: all possible NNI rearragements are tried on the current tree.
NNI will then restart on the tree with the best likelihood, of all
those tried (if there were any). The procedure repeats
until no further likelihood improvements can be obtained. This
strategy tends to produce better results.
Models: Any of the standard
nucleotide,
aminoacid
or codon
models can be selected for the analysis.
Output:
HyPhy will print out the tree string of every rearrangement tried and
the likelihood value for the tree. At the end of the analysis, HyPhy
will either print the improved tree and likelihood, or report that no
improvements could be found. If a better tree is found, the user can
save its Newick string to a file.
Result
Processing Tools: None available.
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