1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
Make a UPGMA cluster
====================
.. sectionauthor:: Catherine Lozupone
An example of how to calculate the pairwise distances for a set of sequences.
**NOTE:** UPGMA should not be used for phylogenetic reconstruction.
.. doctest::
>>> from cogent import LoadSeqs
>>> from cogent.phylo import distance
>>> from cogent.cluster.UPGMA import upgma
Import a substitution model (or create your own)
.. doctest::
>>> from cogent.evolve.models import HKY85
Load the alignment.
.. doctest::
>>> al = LoadSeqs("data/test.paml")
Create a pairwise distances object calculator for the alignment, providing a substitution model instance.
.. doctest::
>>> d = distance.EstimateDistances(al, submodel= HKY85())
>>> d.run(show_progress=False)
Now use this matrix to build a UPGMA cluster.
.. doctest::
>>> mycluster = upgma(d.getPairwiseDistances())
>>> print mycluster.asciiArt()
/-NineBande
/edge.1--|
| | /-HowlerMon
/edge.0--| \edge.2--|
| | \-Human
-root----| |
| \-DogFaced
|
\-Mouse
We demonstrate saving this UPGMA cluster to a file.
.. doctest::
>>> mycluster.writeToFile('test_upgma.tree')
..
We don't actually want to keep that file now, so I'm importing the ``os`` module to delete it.
.. doctest::
:hide:
>>> import os
>>> os.remove('test_upgma.tree')
|
