-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathindex.html
176 lines (160 loc) · 7.05 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
167
168
169
170
171
172
173
174
175
176
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="description" content="Phylocom: Software for
the Analysis of Phylogenetic Community Structure and
Character Evolution"/>
<meta name="keywords" content="Phylocom, phylodiversity,
Cam Webb, Steve Kembel, David Ackerly, comparative methods,
community phylogenetics"/>
<title>Phylocom</title>
<link href="phylocomStyle.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="header">
<h2 align="left">
<img src="phylocom.png" alt="Phylocom logo"
height="90" align="right" />Phylocom
</h2>
<h4 align="left">
Software for the Analysis of Phylogenetic Community Structure
and Character Evolution, with Phylomatic
</h4>
<h5 align="left">Current version: 4.2 (released 2011-08-06)</h5>
<h5 align="left">
© 2011-2017 <a href="http://camwebb.info/">Campbell Webb</a>,
<a href="http://ib.berkeley.edu/labs/ackerly/">David
Ackerly</a>, <a
href="http://kembellab.ca/">Steven
Kembel</a>
</h5>
</div>
<div id="content">
<h3>Features (Current version: 4.2) </h3>
<ul>
<li>
Calculate phylogenetic community structure metrics (Webb's
NRI, NTI, Faith's PD, Rao's entropy) and compare observed
patterns to those expected under various null models of
community assembly and phylogeny structure
(<tt>comstruct</tt>). Now, many metrics incorporate
variation in taxon abundance.
</li>
<li>
Calculate inter-sample phylogenetic distance for
phylogenetic ordination and classification (<tt>comdist</tt> and <tt>comdistnt</tt>). Now incorporates null model testing of observed patterns.
</li>
<li>
Comparative methods for the analysis of character evolution
(<tt>aot</tt>; conservatism metrics, independent contrasts, lineages
through time).
</li>
<li>
Calculate trait distribution metrics within sample
communities and compare to metrics for random community
assembly (<tt>comtrait</tt>).
</li>
<li>
Simulate phylogeny and trait evolution under various evolutionary
models (<tt>ecovolve</tt>).
</li>
<li>
Manipulate phylogenetic trees and ecological community data:
convert Newick to Nexus format, prune and merge
phylogenetic trees, add branch lengths to your supertrees,
community data randomization using one of several null
models, and much more...
</li>
<li>
Turn species lists into phylogenies (with or without branch
lengths) using the included standalone version
of <tt><a href="http://www.phylodiversity.net/phylomatic/">
phylomatic</a></tt>
and <tt>phylocom</tt>'s <tt>bladj</tt> function.
</li>
<li>
Handles large data sets (tested with >10,000
samples/taxa), polytomies, continuous and categorical
characters. NEW: detects UNIX/Windows/Mac line-endings in
your input files.
</li>
</ul>
<p>(Difference from version 4.1 to 4.2: minor bug fixes, and new options: <tt>new2fy</tt> and <tt>nodesigl</tt>)</p>
<h3>Obtaining and running Phylocom </h3>
<p>
The Phylocom distribution consists of C source code, Mac OS X
and Windows binaries, manual, and example files. Read the
manual for assistance installing and running the software.
</p>
<p style="text-align:center;"><a href="https://github.com/phylocom/phylocom/releases"><b>DOWNLOAD
PHYLOCOM & MANUAL</b></a></p>
<p style="text-align:center;">(Also, a <a href="https://github.com/phylocom/phylocom/releases">Chinese
version</a> of the manual, translated by Jinlong Zhang)</p>
<h3 align="left">Development</h3>
<p>We are now using <a href="https://github.com/phylocom/phylocom">github</a> for development and distribution, and welcome pull requests.</p>
<h3 align="left">Support</h3>
<p align="left">If you think you have found a bug, or are
requesting new features, please open an <a href=
"https://github.com/phylocom/phylocom/issues">issue on
github</a>.</p>
<p>For assistance running the software, please subscribe and
post to this mailing list: <a
href="http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net">phylocom-user</a>.
Please <i>read the manual</i> first!
</p>
<p align="left">Other resources:
</p>
<ul>
<li>Sharon Strauss and Jean Burns: <a
href="http://web.archive.org/web/20150703140123/http://bodegaphylo.wikispot.org/Community_Phylogenetics">phylocom
tutorial</a>.
</li>
<li>Steve Vamosi further modified the above: <a href="http://people.ucalgary.ca/~smvamosi/phylocom.htm">phylocom tutorial</a>.
</li>
<li>The <a href="http://picante.r-forge.r-project.org">picante
R package</a> provides several functions for reading and
writing phylocom-formatted data.
</li>
</ul>
<h3 align="left">Citing Phylocom </h3>
<p align="left">If you use results derived from Phylocom
analyses in your publications, please cite:</p>
<ul>
<li>Webb, C. O., Ackerly, D. D. & Kembel, S. W. (2008)
Phylocom: software for the analysis of phylogenetic
community structure and trait evolution. Bioinformatics, 24:
2098-2100. [<a href="http://dx.doi.org/10.1093/bioinformatics/btn358">LINK</a>]
</li>
</ul>
<h3 align="left">License</h3>
<p>
Phylocom is now released under a
Modified (aka Simplified or 3-clause)
<a href="http://www.gnu.org/licenses/license-list.html#ModifiedBSD">BSD
License</a> (as of version 4.0 beta). See also the
<a href="http://www.opensource.org/licenses/bsd-license.php">OSI</a>,
and <a href="http://creativecommons.org/licenses/BSD/">Creative
Commons</a> listings.
</p>
<h3 align="left">Acknowledgments</h3>
<p>
Phylocom development
has been supported by grants 0212873 and 0515520 from the US
<a href="http://www.nsf.gov/">NSF</a>, by <a href="http://www.nserc.ca">
NSERC</a>, by <a href="http://www.arboretum.harvard.edu/">The Arnold
Arboretum of Harvard University</a>, and
the <a href="http://www.yale.edu/yibs/">Yale Institute of
Biospheric Studies</a>. See the manual for full
acknowledgments.
</p>
<script type="text/javascript">
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-34325512-1', 'auto');
ga('send', 'pageview');
</script>
</div>
</body>
</html>