PyloCluster
PyloCluster provides basic functionalities for distance-based clustering procedures in Python, including implementations of the Neighbor-joining and the UPGMA algorithm for phylogenetic reconstruction.
Installation
$ pip install pylocluster
Usage
The following examples requires the python-newick package.
>>> from pylocluster import *
>>> from newick import loads
>>> matrix = squareform([0.5,0.67,0.8,0.2,0.4,0.7,0.6,0.8,0.8,0.3])
>>> nwk = linkage(matrix, taxa=['G', 'S', 'I', 'E', 'D'], method='upgma')
>>> print(loads(nwk).ascii_art())
┌─S
┌───┤
│ └─I
────┤
│ ┌─E
└───┤
│ ┌─G
└───┤
└─D
Release files for pylocluster 0.1.0
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| File | Size | Uploaded | Provenance | Actions |
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| pylocluster-0.1.0.tar.gz | 8.9 kB | Without provenance | Details for pylocluster-0.1.0.tar.gz |
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| pylocluster-0.1.0-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details for pylocluster-0.1.0-py2.py3-none-any.whl |
Total release size: 18.0 kB
Release files / pylocluster-0.1.0.tar.gz
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Release files / pylocluster-0.1.0-py2.py3-none-any.whl
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