biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.TreeConstruction.DistanceMatrix

Distance matrix class that can be used for distance based tree algorithms.

All diagonal elements will be zero no matter what the users provide.

Link to this section Summary

Functions

__init__()

Initialize the class

_set_zero_diagonal()

Set all diagonal elements to zero

format_phylip()

Write data in Phylip format to a given file-like object or handle

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function _set_zero_diagonal()

Set all diagonal elements to zero

Link to this function format_phylip()

Write data in Phylip format to a given file-like object or handle.

The output stream is the input distance matrix format used with Phylip programs (e.g. ‘neighbor’). See: http://evolution.genetics.washington.edu/phylip/doc/neighbor.html

:Parameters:

handle : file or file-like object
    A writeable file handle or other object supporting the 'write'
    method, such as StringIO or sys.stdout. On Python 3, should be
    open in text mode.