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
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
############
The ``apps``
############
``cogent3`` comes with pre-defined "apps" which perform single functions that can be configured by the user. Apps are designed to enable usage without requiring detailed understanding of programming and so they can be applied in batch to a large amount of data. In other words, being able to use them as functions without writing loops or conditionals.
Apps can be used by themselves, or added together to define a "composed function" (aka pipeline). Composed functions can be applied to a single, or thousands, of data file(s).
Apps have several key features
#. trap errors
#. check the validity of input data
#. can be used by themselves or combined into a "composed" app
#. automatically track the relationship between an input data record and its output record
Overview
========
.. toctree::
:maxdepth: 1
app-overview
app-help
app-get
available-apps
dstore
not-completed
The ``progressive_align`` App
=============================
``cogent3`` has a built-in progressive aligner. This is a tree-based HMM aligner that can use any ``cogent3`` substitution model.
.. toctree::
:maxdepth: 1
align-nucleotide
align-codon
align-protein
The ``model`` App
=================
``cogent3`` possesses unique capabilities for molecular evolutionary analyses. Of particular significance are our non-stationary model classes and the associated measurement of genetic distance from these. That said, we also implement most of the conventional substitution models. See ``cogent3.available_models()`` for a display of the built-in models.
You can use these models either through the general ``model`` app, or some task specific apps. Both are described below.
.. toctree::
:maxdepth: 1
evo-model
evo-model-with-tree
evo-model-timehet
evo-extract-model-stats
evo-ancestral-states
evo-dt-nuc-model
evo-tr-nuc-model
evo-nstat-codon-model
evo-tr-codon-model
The ``hypothesis`` App
======================
Takes two (or more) ``model`` instances and performs hypothesis test.
.. toctree::
:maxdepth: 1
evo-hypothesis
The ``natsel`` Apps
===================
These apps all employ codon models to evaluate different types of hypotheses regarding the mode of natural selection.
.. toctree::
:maxdepth: 1
evo-natsel_neutral
evo-natsel_timehet
evo-natsel_sitehet
evo-natsel_zhang
Write your own Apps
===================
You can write your own apps.
.. toctree::
:maxdepth: 1
user_function
|
