phyloworks.github.io/software.html at master · phyloworks/phyloworks.github.io · GitHub

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
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208

<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">
    <meta name="description" content="">
    <meta name="author" content="">
    <link rel="icon" type="image/png" href="favicon.png"/>

    <title>Heath Lab – EEOB – Iowa State University</title>

    <!-- Bootstrap core CSS -->
    <link href="./css/bootstrap.min.css" rel="stylesheet">

    <!-- Custom styles for this template -->
    <link href="navbar-fixed-top.css" rel="stylesheet">

  </head>

  <body>

    <!-- fixed navbar -->
    <div class="navbar navbar-default navbar-fixed-top" role="navigation">
      <div class="container">
        <div class="navbar-header">
          <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
            <span class="sr-only">Toggle navigation</span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
          </button>
          <a class="navbar-brand" href="index.html">Heath Lab @ ISU</a>
        </div>
        <div class="navbar-collapse collapse">
          <ul class="nav navbar-nav">
            <li><a href="index.html">Home</a></li>
            <li><a href="research.html">Research</a></li>
            <li><a href="people.html">People</a></li>
            <li><a href="publications.html">Publications</a></li>
            <li class="active"><a href="software.html">Software</a></li>
            <li class="dropdown">
              <a href="#" class="dropdown-toggle" data-toggle="dropdown">Resources <span class="caret"></span></a>
              <ul class="dropdown-menu" role="menu">
                <li><a href="resources/links.html">Links</a></li>
                <li><a href="resources/collaborators.html">Collaborators</a></li>
                <li class="divider"></li>
                <li class="dropdown-header"><font color="white">Teaching</font></li>
                <li><a href="resources/workshops.html">Workshops</a></li>
                <li class="divider"></li>
                <li class="dropdown-header"><font color="white">Join the Heath Lab</font></li>
                <li><a href="resources/gradschool.html">Graduate Programs</a></li>
                <li><a href="resources/postdocinfo.html">Postdoc Opportunities</a></li>
              </ul>
            </li>
          </ul>
          <ul class="nav navbar-nav navbar-right">
            <li><a href="http://www.eeob.iastate.edu/">EEOB</a></li>
            <li><a href="http://www.iastate.edu/">ISU</a></li>
          </ul>
        </div><!--/.nav-collapse -->
      </div>
    </div>


    <div class="container">


	<div class="page-header">
        <h1 id="what">Software</h1>
    </div>
      <div class="jumbotron">
        <p>My primary approach to developing phylogenetic tools is to apply new statistical models as priors using Bayesian inference methods. The implementation of complex models in a Bayesian
		framework provides a flexible way to model evolutionary processes and obtain reliable estimates of biological parameters. When coupled with numerical methods––such as Markov chain Monte Carlo (MCMC)––for
		approximating the posterior probability distribution of parameters, Bayesian inference methods can be extremely powerful and have revolutionized the range of evolutionary questions that can be tackled.
		</p>
		<p>
		Statistical phylogenetic inference is heavily computational, thus the software I develop is written in C++ (a compiled language).
		I also write small accessory programs for summarizing MCMC, simulation, or plotting data in Python.
		</p>
		<p>
		I am dedicated to contributing open-source software products for academic research. My current software projects are available on <a href="https://github.com/trayc7">GitHub</a>.
		</p>
      </div>

        <div class="row">
            <div class="col-lg-12">
                <h2 class="page-header">RevBayes
                </h2>
			  <div class="well">
			  	<p><a href="https://github.com/revbayes/revbayes"><img src="images/github.png" alt="" width="30" /> https://github.com/revbayes/revbayes</a>
			  	</p>
				<p>RevBayes is a Bayesian inference framework. It is primarily for phylogenetic inference using integrative models
				and MCMC.
				</p>
			  </div>
           </div>
        </div>

        <div class="row">
            <div class="col-lg-12">
                <h2 class="page-header">DPPDiv
                </h2>
			  <div class="well">
				<p><a href="https://github.com/trayc7/DPPDiv"><img src="images/github.png" alt="" width="30" /> https://github.com/trayc7/DPPDiv</a>
			  	</p>
			  	<p>DPPDiv is a program for estimating species divergence times and lineage-specific substitution rates on a fixed topology. The prior on branch rates is a Dirichlet process prior which clusters branches into distinct rate classes. Alternative priors including the global molecular clock and the independent rates model are also available. The priors on node ages include the birth-death (and Yule) model and the uniform distribution.
				</p>
				<p>
				DPPDiv user discussion email list: <a href="https://groups.google.com/d/forum/dppdiv-users">https://groups.google.com/d/forum/dppdiv-users</a>
				</p>
			<h4>Descriptions of models and implementation</h4>

			<ul>
				<li><b>Heath</b>, Huelsenbeck, Stadler. 2014. <a href="http://www.pnas.org/content/111/29/E2957.abstract">The fossilized birth-death process for coherent calibration of divergence-time estimates</a>. <i>Proceedings of the National Academy of Sciences</i> 111(29):E2957–E2966. [<a href="http://arxiv.org/abs/1310.2968">arXiv preprint arXiv:1310.2968</a>] </li>
				<li><b>Heath</b>, Holder, Huelsenbeck. 2012. <a href="http://mbe.oxfordjournals.org/content/29/3/939">A Dirichlet process prior for estimating lineage-specific substitution rates.</a> <i>Molecular Biology and Evolution</i> 29:939-955. [<a href="http://phylo.bio.ku.edu/sites/default/files/Heath_etal_MBE_2012.pdf">pdf</a>]</li>
				<li><b>Heath</b>. 2012. <a href="http://sysbio.oxfordjournals.org/content/61/5/793">A hierarchical Bayesian model for calibrating estimates of species divergence times.</a> <i>Systematic Biology</i> 61:793-809. [<a href="http://phylo.bio.ku.edu/sites/default/files/Heath_SystBiol_2012.pdf">pdf</a>]</li>
				<li>Darriba, Aberer, Flouri, <b>Heath</b>, Izquierdo-Carrasco, Stamatakis. 2013. <a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6650929">Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library</a>. <i>Parallel and Distributed Processing Symposium Workshops PhD Forum (IPDPSW)</i>, 2013 IEEE 27th International, Boston, USA, pp. 539-548. (peer-reviewed conference paper) [<a href="http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-2.pdf">pdf</a>]</li>
				<li>Flouri, Stamatakis. 2012. <a href="http://sco.h-its.org/exelixis/rrdr2012-7.php">An Improvement to DPPDIV.</a> Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-7. (Technical report on optimization and parallelization of DPPDiv)</li>
			<ul/>
			</p>
			  </div>
           </div>
        </div>

        <div class="row">
            <div class="col-lg-12">
                <h2 class="page-header">FossilGen
                </h2>
			  <div class="well">
			  <p><a href="https://github.com/trayc7/FossilGen"><img src="images/github.png" alt="" width="30" /> https://github.com/trayc7/FossilGen</a>
			  	</p>
				<p>FossilGen is a program for simulating phylogenies and fossil occurrence times under the serial-sampled birth-death process of Stadler (J. Ther. Biol, 2010).</p>
			  </div>
           </div>
        </div>

<!--
        <div class="row">
            <div class="col-lg-12">
                <h2 class="page-header">Other projects
                </h2>
			  	list
           </div>
        </div>
 -->


        <hr>
        <!-- Footer -->
        <footer>
            <div class="row">
                <div class="col-md-3 col-sm-12">
                    <a rel="license" href="https://github.com/phyloworks/phyloworks.github.io"><img style="border-width:0" src="images/Octocat.png" alt="" width="60" /></a><br>Hosted by <a href="https://github.com/">GitHub</a> Pages.
                	<br>Theme based on <a href="http://getbootstrap.com/">Bootstrap</a>, <a href="https://kuler.adobe.com/purple-haze-color-theme-57997/">Adobe Kuler 57997</a>, & <a href="http://paintstrap.com/">PaintStrap</a>.
                    <br>
                    <br>
                </div>
                <!-- /.col-lg-12 -->
                <div class="col-md-6 col-sm-12">
                	<center><a href="http://phylopic.org/image/6c9cb19d-1d8a-4215-88ba-d49cd4917a5e/"><img src="http://phylopic.org/assets/images/submissions/6c9cb19d-1d8a-4215-88ba-d49cd4917a5e.512.png" alt="" width="80" /></a>
                    <br>
                    <br>
                    </center>
                </div>
                <div class="col-md-3 col-sm-12">
                	<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />Except where otherwise noted, content on this site is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
                    <br>
                    <br>
                </div>
                <!-- /.col-lg-12 -->
            </div>
            <!-- /.row -->
        </footer>


    </div> <!-- /container -->


    <!-- Bootstrap core JavaScript
    ================================================== -->
    <!-- Placed at the end of the document so the pages load faster -->
    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
    <script src="./js/bootstrap.min.js"></script>
    <script src="../../assets/js/docs.min.js"></script>
    <!-- IE10 viewport hack for Surface/desktop Windows 8 bug -->
    <script src="../../assets/js/ie10-viewport-bug-workaround.js"></script>
    <!-- Start of StatCounter Code for Default Guide -->
<script type="text/javascript">
var sc_project=10040953;
var sc_invisible=1;
var sc_security="62c272e1";
var scJsHost = (("https:" == document.location.protocol) ?
"https://secure." : "http://www.");
document.write("<sc"+"ript type='text/javascript' src='" +
scJsHost+
"statcounter.com/counter/counter.js'></"+"script>");
</script>
<noscript><div class="statcounter"><a title="website
statistics" href="http://statcounter.com/"
target="_blank"><img class="statcounter"
src="http://c.statcounter.com/10040953/0/62c272e1/1/"
alt="website statistics"></a></div></noscript>
<!-- End of StatCounter Code for Default Guide -->
  </body>
</html>