Handel Package

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Handel Package

Handel: an evolutionary model-based Statistical Alignment package.

  • Main program:
    • handalign - program to sample multiple alignments, phylogenies, and parameters. Currently the main supported program in the Handel package. See HandAlign transducer for a depiction of the underlying model.
      • Input:

* either unaligned sequences (Fasta Format), or (optionally) an alignment (Stockholm Format) which may include an embedded tree (Newick Format) * optional rate matrix (Xrate Format)

      • Output:

* final or best alignment (Stockholm Format) with embedded tree (Newick Format) and model parameters * (optionally) an MCMC sampling trace of all alignments/trees/parameters visited (Stockholm Format + Newick Format)

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