CINXE.COM

<!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" xml:lang="en" lang="en" dir="ltr"> <head><script type="text/javascript" src="https://web-static.archive.org/_static/js/bundle-playback.js?v=7YQSqjSh" charset="utf-8"></script> <script type="text/javascript" src="https://web-static.archive.org/_static/js/wombat.js?v=txqj7nKC" charset="utf-8"></script> <script>window.RufflePlayer=window.RufflePlayer||{};window.RufflePlayer.config={"autoplay":"on","unmuteOverlay":"hidden"};</script> <script type="text/javascript" src="https://web-static.archive.org/_static/js/ruffle/ruffle.js"></script> <script type="text/javascript"> __wm.init("https://web.archive.org/web"); __wm.wombat("http://wikiomics.org/wiki/Building_phylogenetic_trees","20070920172452","https://web.archive.org/","web","https://web-static.archive.org/_static/", "1190309092"); </script> <link rel="stylesheet" type="text/css" href="https://web-static.archive.org/_static/css/banner-styles.css?v=p7PEIJWi" /> <link rel="stylesheet" type="text/css" href="https://web-static.archive.org/_static/css/iconochive.css?v=3PDvdIFv" />  <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <meta name="KEYWORDS" content="Building phylogenetic trees"/> <meta name="robots" content="index,follow"/> <link rel="shortcut icon" href="/web/20070920172452im_/http://wikiomics.org/favicon.ico"/> <link title="Creative Commons" type="application/rdf+xml" href="/index.php?title=Building_phylogenetic_trees&action=creativecommons" rel="meta"/> <link rel="copyright" href="https://web.archive.org/web/20070920172452/http://www.gnu.org/copyleft/fdl.html"/> <title>Building phylogenetic trees - Wikiomics Bioinformatics Wiki</title> <style type="text/css" media="screen,projection">/*<![CDATA[*/ @import "/web/20070920172452cs_/http://wikiomics.org/skins/monobook/main.css"; /*]]>*/</style> <link rel="stylesheet" type="text/css" media="print" href="/web/20070920172452cs_/http://wikiomics.org/skins/common/commonPrint.css"/>     <script type="text/javascript" src="/web/20070920172452js_/http://wikiomics.org/index.php?title=-&action=raw&gen=js"></script> <script type="text/javascript" src="/web/20070920172452js_/http://wikiomics.org/skins/common/wikibits.js"></script> <style type="text/css">/*<![CDATA[*/ @import "/web/20070920172452cs_/http://wikiomics.org/index.php?title=MediaWiki:Monobook.css&action=raw&ctype=text/css&smaxage=18000"; @import "/web/20070920172452cs_/http://wikiomics.org/index.php?title=-&action=raw&gen=css&maxage=18000"; /*]]>*/</style> </head> <body class="ns-0"> <div id="globalWrapper"> <div id="column-content"> <div id="content"> <a name="top" id="top"></a> <h1 class="firstHeading">Building phylogenetic trees</h1> <div id="bodyContent"> <h3 id="siteSub">From Wikiomics</h3> <div id="contentSub"></div>  <p>For a excellent background on <a href="/web/20070920172452/http://wikiomics.org/wiki/Phylogenetics" title="Phylogenetics">Phylogenetics</a> see the relevant <a href="https://web.archive.org/web/20070920172452/http://en.wikipedia.org/wiki/Phylogenetics" class="external text" title="http://en.wikipedia.org/wiki/Phylogenetics" rel="nofollow">Phylogenetics</a> and <a href="https://web.archive.org/web/20070920172452/http://en.wikipedia.org/wiki/Computational_phylogenetics" class="external text" title="http://en.wikipedia.org/wiki/Computational phylogenetics" rel="nofollow">computational phylogenetics</a> articles at Wikipedia. Joe Felsenstein maintains a rather complete list of <a href="https://web.archive.org/web/20070920172452/http://evolution.genetics.washington.edu/phylip/software.html" class="external text" title="http://evolution.genetics.washington.edu/phylip/software.html" rel="nofollow">phylogeny software</a>. </p> <ul><li> <a href="https://web.archive.org/web/20070920172452/http://evolution.genetics.washington.edu/phylip.html" class="external text" title="http://evolution.genetics.washington.edu/phylip.html" rel="nofollow">Phylip</a> a free package of programs for inferring phylogenies. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. </li></ul> <ul><li> <a href="https://web.archive.org/web/20070920172452/http://mrbayes.csit.fsu.edu/" class="external text" title="http://mrbayes.csit.fsu.edu/" rel="nofollow">MrBayes</a> is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. </li></ul>  <div class="printfooter"> Retrieved from "<a href="https://web.archive.org/web/20070920172452/http://wikiomics.org/wiki/Building_phylogenetic_trees">http://wikiomics.org/wiki/Building_phylogenetic_trees</a>"</div> <div id="catlinks"><p class="catlinks"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Special:Categories&article=Building_phylogenetic_trees" title="Special:Categories">Categories</a>: <a href="/web/20070920172452/http://wikiomics.org/wiki/Category:Sequence" title="Category:Sequence">Sequence</a> | <a href="/web/20070920172452/http://wikiomics.org/wiki/Category:Phylogenetics" title="Category:Phylogenetics">Phylogenetics</a></p></div>  <div class="visualClear"></div> </div> </div> </div> <div id="column-one"> <div id="p-cactions" class="portlet"> <h5>Views</h5> <ul> <li id="ca-nstab-main" class="selected"><a href="/web/20070920172452/http://wikiomics.org/wiki/Building_phylogenetic_trees">Article</a></li><li id="ca-talk" class="new"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Talk:Building_phylogenetic_trees&action=edit">Discussion</a></li><li id="ca-viewsource"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Building_phylogenetic_trees&action=edit">View source</a></li><li id="ca-history"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Building_phylogenetic_trees&action=history">History</a></li> </ul> </div> <div class="portlet" id="p-personal"> <h5>Personal tools</h5> <div class="pBody"> <ul> <li id="pt-login"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Special:Userlogin&returnto=Building_phylogenetic_trees">Create an account or log in</a></li> </ul> </div> </div> <div class="portlet" id="p-logo"> <a style="background-image: url(/web/20070920172452im_/http://wikiomics.org/skins/common/images/wikiomics135x135.png);" href="/web/20070920172452/http://wikiomics.org/wiki/Main_Page" title="Main Page"></a> </div> <script type="text/javascript"> if (window.isMSIE55) fixalpha(); </script> <div class="portlet" id="p-navigation"> <h5>Navigation</h5> <div class="pBody"> <ul> <li id="n-mainpage"><a href="/web/20070920172452/http://wikiomics.org/wiki/Main_Page">Main Page</a></li> <li id="n-listofarticles"><a href="/web/20070920172452/http://wikiomics.org/wiki/List_of_articles">List of articles</a></li> <li id="n-portal"><a href="/web/20070920172452/http://wikiomics.org/wiki/Wikiomics:Community_Portal">Community portal</a></li> <li id="n-recentchanges"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Recentchanges">Recent changes</a></li> <li id="n-randompage"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Random">Random page</a></li> <li id="n-sandbox"><a href="/web/20070920172452/http://wikiomics.org/wiki/Sandbox">Sandbox</a></li> <li id="n-mailing-list"><a href="https://web.archive.org/web/20070920172452/http://groups.google.com/group/wikiomics">Mailing-list</a></li> <li id="n-help"><a href="/web/20070920172452/http://wikiomics.org/wiki/Help:Contents">Help</a></li> </ul> </div> </div> <div id="p-search" class="portlet"> <h5><label for="searchInput">Search</label></h5> <div class="pBody"> <form name="searchform" action="/web/20070920172452/http://wikiomics.org/wiki/Special:Search" id="searchform"> <input id="searchInput" name="search" type="text" accesskey="f" value=""/> <input type="submit" name="go" class="searchButton" id="searchGoButton" value="Go"/> <input type="submit" name="fulltext" class="searchButton" value="Search"/> </form> </div> </div> <div class="portlet" id="p-tb"> <h5>Toolbox</h5> <div class="pBody"> <ul> <li id="t-whatlinkshere"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Whatlinkshere/Building_phylogenetic_trees">What links here</a></li> <li id="t-recentchangeslinked"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Recentchangeslinked/Building_phylogenetic_trees">Related changes</a></li> <li id="t-upload"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Upload">Upload file</a></li> <li id="t-specialpages"><a href="/web/20070920172452/http://wikiomics.org/wiki/Special:Specialpages">Special pages</a></li> <li id="t-print"><a href="/web/20070920172452/http://wikiomics.org/index.php?title=Building_phylogenetic_trees&printable=yes">Printable version</a></li> </ul> </div> </div> </div> <div class="visualClear"></div> <div id="footer"> <div id="f-poweredbyico"><a href="https://web.archive.org/web/20070920172452/http://www.mediawiki.org/"><img src="/web/20070920172452im_/http://wikiomics.org/skins/common/images/poweredby_mediawiki_88x31.png" alt="MediaWiki"/></a></div> <div id="f-copyrightico"><a href="https://web.archive.org/web/20070920172452/http://www.gnu.org/copyleft/fdl.html"><img src="/web/20070920172452im_/http://wikiomics.org/skins/common/images/gnu-fdl.png" alt="GNU Free Documentation License 1.2"/></a></div> <ul id="f-list"> <li id="f-lastmod"> This page was last modified 10:05, 13 September 2006.</li> <li id="f-viewcount">This page has been accessed 448 times.</li> <li id="f-copyright">Content is available under <a href="https://web.archive.org/web/20070920172452/http://www.gnu.org/copyleft/fdl.html" class="external " title="http://www.gnu.org/copyleft/fdl.html" rel="nofollow">GNU Free Documentation License 1.2</a>.</li> <li id="f-about"><a href="/web/20070920172452/http://wikiomics.org/wiki/Wikiomics:About" title="Wikiomics:About">About Wikiomics</a></li> <li id="f-disclaimer"><a href="/web/20070920172452/http://wikiomics.org/wiki/Wikiomics:General_disclaimer" title="Wikiomics:General disclaimer">Disclaimers</a></li> </ul> </div> </div>  </body> </html>