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
65
66
67
68
69
70
71
72
73
74
75
76
77
|
************************************
Controlling third party applications
************************************
Existing supported apps
=======================
Alignment apps
--------------
clustalw and muscle
^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import LoadSeqs, DNA
>>> from cogent.app.clustalw import align_unaligned_seqs as clustal_aln
>>> from cogent.app.muscle import align_unaligned_seqs as muscle_aln
>>> seqs = LoadSeqs(filename='data/test2.fasta', aligned=False)
>>> aln1 = clustal_aln(seqs, DNA)
>>> aln2 = muscle_aln(seqs, DNA)
>>> aln1 == aln2
True
>>> from cogent.app.fasttree import build_tree_from_alignment
>>> tr = build_tree_from_alignment(aln1,moltype=DNA)
>>> print tr.asciiArt()
/-Mouse
|
---------|--NineBande
|
| /-DogFaced
\0.678---|
| /-HowlerMon
\0.720---|
\-Human
And if you have matplotlib installed you can draw the tree (see :ref:`draw-trees`).
.. TODO add in cross-ref to drawing usage example
BLAST
-----
See :ref:`blast-usage`.
Phylo apps
----------
*To be written.*
RNA structure apps
------------------
*To be written.*
Visualisation
-------------
*To be written.*
PyMol, MAGE
^^^^^^^^^^^
Adding new apps
===============
*To be written.*
Pipelining 3rd party apps
=========================
*To be written.*
.. integrating with cogent features
.. grab seqs from genbank, align, build tree, cogent evolutionary analysis
|
