Navigation Banner
 

      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.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002