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hashrf

source 

.hashrf(
   file, n_trees, output_file
)

Computes unweighted Robinson Foulds distances

Args

  • file (str) : name of input file with phylogenetic trees in newick format
  • n_trees (int) : number of trees in file
  • output_file (str) : name of output file that will contain the distance matrix

Returns

  • distance_matrix (numpy.ndarray) : computed distance matrix

Raises

  • PearExecutableError : if hashrf cannot be run, or fails, or produces output that does not match n_trees.

hashrf_weighted

source 

.hashrf_weighted(
   file, n_trees, output_file
)

Computes weighted Robinson Foulds distances

Args

  • file (str) : name of input file with phylogenetic trees in newick format
  • n_trees (int) : number of trees in file
  • output_file (str) : name of output file that will contain the distance matrix

Returns

  • distance_matrix (numpy.ndarray) : computed distance matrix

Raises

  • PearExecutableError : if hashrf cannot be run, or fails, or produces output that does not match n_trees.