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
94
95
96
97
98
99
100
101
102
|
#####################
Cogent Usage Examples
#####################
**************************************
A Note on the Computable Documentation
**************************************
The following examples are all available as standalone text files which can be computed using the Python doctest module.
*****************
Data manipulation
*****************
.. toctree::
:maxdepth: 1
translate_dna
seq_features
complete_seq_features
reverse_complement
align_codons_to_protein
aln_profile
genetic_code_aa_index
handling_tabular_data
handling_3dstructures
entity_selection
query_ncbi
query_ensembl
manipulating_tree_nodes
**********************************
Controlling 3rd party applications
**********************************
.. toctree::
:maxdepth: 1
application_controller_framework
alignment_app_controllers
phylogeny_app_controllers
generating_app_commandlines
*********************
General data analysis
*********************
.. toctree::
:maxdepth: 1
goodness_of_fit
perform_PCoA_analysis
perform_nmds
motif_results
unifrac
******************
Data Visualisation
******************
.. toctree::
:maxdepth: 1
draw_dendrogram
draw_dotplot
*******************
Modelling Evolution
*******************
.. toctree::
:maxdepth: 1
simple
relative_rate
neutral_test
scope_model_params_on_trees
codon_models
empirical_protein_models
testing_multi_loci
reuse_results
unrestricted_nucleotide
simulate_alignment
parametric_bootstrap
estimate_startingpoint
coevolution
rate_heterogeneity
hmm_par_heterogeneity
***************************
Phylogenetic Reconstruction
***************************
.. toctree::
:maxdepth: 1
calculate_pairwise_distances
calculate_neigbourjoining_tree
calculate_UPGMA_cluster
phylo_by_ls
maketree_from_proteinseqs
|
