-
Notifications
You must be signed in to change notification settings - Fork 3
/
index.html
166 lines (146 loc) · 9.63 KB
/
index.html
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
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Welcome to PyCogent’s documentation! — PyCogent 1.9 documentation</title>
<link rel="stylesheet" href="_static/agogo.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '1.9',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="PyCogent 1.9 documentation" href="#" />
<link rel="next" title="Quick installation using pip" href="install.html" />
<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRQZ4X-jPDmWcshBrz2j7-fJvuUABRTGWmdiw2G89JpgztGlFGG8hDxRAw"></script>\
<script type="text/javascript" src="_static/google_feed.js"></script>
</head>
<body role="document">
<div class="header-wrapper" role="banner">
<div class="header">
<div class="headertitle"><a
href="#">PyCogent 1.9 documentation</a></div>
<div class="rel" role="navigation" aria-label="related navigation">
<a href="install.html" title="Quick installation using pip"
accesskey="N">next</a> |
<a href="genindex.html" title="General Index"
accesskey="I">index</a>
</div>
</div>
</div>
<div class="content-wrapper">
<div class="content">
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="welcome-to-pycogent-s-documentation">
<span id="contents"></span><h1>Welcome to PyCogent’s documentation!<a class="headerlink" href="#welcome-to-pycogent-s-documentation" title="Permalink to this headline">¶</a></h1>
<p><strong>Contents</strong></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="install.html">Quick installation using pip</a></li>
<li class="toctree-l1"><a class="reference internal" href="README.html">The Readme</a></li>
<li class="toctree-l1"><a class="reference internal" href="coding_guidelines.html">Coding guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="data_file_links.html">The data files used in the documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Cogent Usage Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="cookbook/index.html">PyCogent Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer_notes.html">For Developers</a></li>
<li class="toctree-l1"><a class="reference internal" href="scripting_guidelines.html">Scripting guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="licenses.html">Licenses and disclaimer</a></li>
<li class="toctree-l1"><a class="reference internal" href="ChangeLog.html">Changelog</a></li>
</ul>
</div>
<div class="section" id="overview">
<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
<p>PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.</p>
<p>Our primary goal is to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets. The project is routinely employed in numerous labs across the world and has provided essential capabilities for many high profile publications, e.g. <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/19043404?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">Nature 2009 457:480-4</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/19004758?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">PNAS 2008 105:17994-9</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/18497261?ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">Science 2008 320:1647-51</a>, <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/18464734?dopt=Citation">Nature 2008 453: 175-83</a> and <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/17828264?dopt=Citation">Nat Genet 2007 39: 1261-5</a>.</p>
</div>
<div class="section" id="contacts-and-contributing">
<h2>Contacts and contributing<a class="headerlink" href="#contacts-and-contributing" title="Permalink to this headline">¶</a></h2>
<p>If you find a bug or have feature/documentation requests, please create a new issue on our GitHub <a class="reference external" href="https://github.com/pycogent/pycogent/issues">issue tracker</a>. If you have any questions, please create a new issue on the <a class="reference external" href="https://github.com/pycogent/pycogent/issues">issue tracker</a> and tag it with the <em>question</em> tag. We appreciate your input!</p>
</div>
<div class="section" id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this headline">¶</a></h2>
<p>If you use this software for published work please cite – <a class="reference external" href="http://genomebiology.com/2007/8/8/R171">Knight et al., 2007, Genome Biol, 8, R171</a>.</p>
</div>
<div class="section" id="search">
<h2>Search<a class="headerlink" href="#search" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
</ul>
</div>
<div class="section" id="news-and-announcements">
<h2>News and Announcements<a class="headerlink" href="#news-and-announcements" title="Permalink to this headline">¶</a></h2>
<p>PyCogent News and Announcements are available via the News and Announcements Blog at <a class="reference external" href="http://pycogent.wordpress.com">http://pycogent.wordpress.com</a>.</p>
<p><a class="reference external" href="http://pycogent.wordpress.com/feed">Subscribe to the News and Annoucements RSS Feed</a></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="sidebar">
<div class="news">
<table id="feed"><tr><td><h3><a href="http://pycogent.wordpress.com/">PyCogent News and Announcements</a></h3></td>
</tr></table></div>
<h3>Table Of Contents</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="install.html">Quick installation using pip</a></li>
<li class="toctree-l1"><a class="reference internal" href="README.html">The Readme</a></li>
<li class="toctree-l1"><a class="reference internal" href="coding_guidelines.html">Coding guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="data_file_links.html">The data files used in the documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Cogent Usage Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="cookbook/index.html">PyCogent Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer_notes.html">For Developers</a></li>
<li class="toctree-l1"><a class="reference internal" href="scripting_guidelines.html">Scripting guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="licenses.html">Licenses and disclaimer</a></li>
<li class="toctree-l1"><a class="reference internal" href="ChangeLog.html">Changelog</a></li>
</ul>
<div role="search">
<h3 style="margin-top: 1.5em;">Search</h3>
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="clearer"></div>
</div>
</div>
<div class="footer-wrapper">
<div class="footer">
<div class="left">
<div role="navigation" aria-label="related navigaton">
<a href="install.html" title="Quick installation using pip"
>next</a> |
<a href="genindex.html" title="General Index"
>index</a>
</div>
<div role="note" aria-label="source link">
<br/>
<a href="_sources/index.txt"
rel="nofollow">Show Source</a>
</div>
</div>
<div class="right">
<div class="footer" role="contentinfo">
© Copyright 2016, PyCogent Team.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.1.
</div>
</div>
<div class="clearer"></div>
</div>
</div>
</body>
</html>