¶

quartet¶

source

.quartet(
   file, n_trees, output_file
)

Computes quartet 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 tqDist cannot be run, fails, or produces a matrix that does not match n_trees.

triplet¶

source

.triplet(
   file, n_trees, output_file
)

Computes triplet 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 tqDist cannot be run, fails, or produces a matrix that does not match n_trees.