fileformat : {‘csv’, ‘tre’,’nwk’,’dst’, ‘taxa’, ‘starling’, ‘paps.nex’, ‘paps.csv’}
The format that is written to file. This corresponds to the file
extension, thus ‘csv’ creates a file in csv-format, ‘dst’ creates
a file in Phylip-distance format, etc.
filename : str
Specify the name of the output file (defaults to a filename that
indicates the creation date).
subset : bool (default=False)
If set to c{True}, return only a subset of the data. Which subset
is specified in the keywords ‘cols’ and ‘rows’.
cols : list
If subset is set to c{True}, specify the columns that shall be
written to the csv-file.
rows : dict
If subset is set to c{True}, use a dictionary consisting of keys
that specify a column and values that give a Python-statement in
raw text, such as, e.g., “== ‘hand’”. The content of the specified
column will then be checked against statement passed in the
dictionary, and if it is evaluated to c{True}, the respective row
will be written to file.
cognates : str
Name of the column that contains the cognate IDs if ‘starling’ is
chosen as an output format.
missing : { str, int } (default=0)
If ‘paps.nex’ or ‘paps.csv’ is chosen as fileformat, this character
will be inserted as an indicator of missing data.
tree_calc : {‘neighbor’, ‘upgma’}
If no tree has been calculated and ‘tre’ or ‘nwk’ is chosen as
output format, the method that is used to calculate the tree.
threshold : float (default=0.6)
The threshold that is used to carry out a flat cluster analysis if
‘groups’ or ‘cluster’ is chosen as output format.
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