This documentation is for version 2.0.dev, which is not released yet.
Carry out a cluster analysis based on the UPGMA algorithm (Sokal1958).
Parameters : | matrix : or numpy.array
taxa : list
distances : bool
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Returns : | newick : str
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See also
lingpy.algorithm.cluster.neighbor, lingpy.algorithm.cluster.flat_upgma
Examples
Function is automatically imported when importing lingpy.
>>> from lingpy import *
Create an arbitrary of taxa.
>>> taxa = ['German','Swedish','Icelandic','English','Dutch']
Create an arbitrary matrix.
>>> matrix = squareform([0.5,0.67,0.8,0.2,0.4,0.7,0.6,0.8,0.8,0.3])
Carry out the cluster analysis.
>>> upgma(matrix,taxa,distances=False)
'((Swedish,Icelandic),(English,(German,Dutch)));'