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<!DOCTYPE html> <html lang="en-gb"> <head> <title>Super trees</title> <link rel="stylesheet" type="text/css" media="all" href="/minified/1627d0642fc0489f4d5171e89c120c90.css"/><link rel="stylesheet" type="text/css" media="all" href="/minified/1e7dbc57580167c82fbefd42000cbfd3.image.css"/> <link href="/i/ensembl-favicon.png" type="image/png" rel="icon" /> <link href="/apple-touch-icon.png" type="image/png" rel="apple-touch-icon" /> <link rel="search" type="application/opensearchdescription+xml" title="Ensembl (All)" href="//metazoa.ensembl.org/opensearch/all.xml" /> <meta name="description" content="Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest" /> <meta name="viewport" content="target-densitydpi=device-dpi, width=device-width, initial-scale=1.0, maximum-scale=2.0, user-scalable=yes" /> <script>var prefetch = [];</script> </head> <body id="ensembl-webpage" class="ie ie7 ie67 static" data-pace="2"> <div id="min_width_container"> <div id="min_width_holder">   <div id="masthead" class="js_panel"> <input type="hidden" class="panel_type" value="Masthead" /> <div class="logo_holder"><a href="/"><img src="/i/e.png" alt="Ensembl Genomes Home" title="Ensembl Genomes Home" class="print_hide" style="width:43px;height:40px" /></a><a href="/"><img src="/i/ensemblMetazoa.png" alt="Ensembl Metazoa Home" title="Ensembl Metazoa Home" class="print_hide" style="width:195px;height:40px" /></a><img src="/i/e-ensembl_print.gif" alt="Ensembl Metazoa Home" title="Ensembl Metazoa Home" class="screen_hide_inline" style="width:195px;height:40px" /> <span class="print_hide"> <span id="site_menu_button">▼</span> <ul id="site_menu" style="display:none"> <li><a href="http://www.ensemblgenomes.org">Ensembl Genomes</a></li> <li><a href="http://bacteria.ensembl.org">Ensembl Bacteria</a></li> <li><a href="http://protists.ensembl.org">Ensembl Protists</a></li> <li><a href="http://fungi.ensembl.org">Ensembl Fungi</a></li> <li><a href="http://plants.ensembl.org">Ensembl Plants</a></li> <li><a href="http://metazoa.ensembl.org">Ensembl Metazoa</a></li> <li><a href="http://www.ensembl.org">Ensembl (vertebrates)</a></li> </ul> </span> </div> <div class="mh print_hide"> <div class="account_holder"><div class="_account_holder"><div class="account-loading">Loading…</div><form action="/Ajax/accounts_dropdown"></form></div></div> <div class="tools_holder"><ul class="tools"><li><a class="constant" href="/hmmer">HMMER</a></li><li><a class="constant" href="/Multi/Tools/Blast">BLAST</a></li><li><a class="constant" href="/biomart/martview">BioMart</a></li><li><a class="constant" href="/tools.html">Tools</a></li><li><a class="constant" href="/info/data/ftp/index.html">Downloads</a></li><li><a class="constant" href="/info/">Help & Docs</a></li><li class="last"><a class="constant" target="_blank" href="http://www.ensembl.info">Blog</a></li></ul><div class="more"><a href="#">More <span class="arrow">▼</span></a></div></div> <div class="search_holder print_hide"> <div id="searchPanel" class="js_panel"> <input type="hidden" class="panel_type" value="SearchBox" /> <form action="/Multi/Psychic"> <div class="search print_hide"> <div class="sites button"> <img class="search_image no-sprite badge-16" src="/i/search/ensemblunit.gif" alt="" /> <img src="/i/search/down.gif" style="width:7px" alt="" /> <input type="hidden" name="site" value="ensemblunit" /> </div> <div> <label class="hidden" for="se_q">Search terms</label> <input class="query inactive" id="se_q" type="text" name="q" value="Search Ensembl Metazoa…" data-role="none" onkeydown="if (event.keyCode == 13) { $(this).closest('form').submit(); 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Both our <a href="homology_method.html">protein trees</a> and <a href="ncRNA_methods.html">ncRNA trees</a> resources contain super trees. </p> <p>They arise from two situations</p> <ol> <li>a dynamic process to cater for large families,</li> <li>the handling of some Panther sub-families</li> </ol> <p> In both cases (see below), we infer some homologies across the super tree, which means that two orthologues or paralogues may be in <em>different</em> gene trees. </p> <h2 id="breakingdownlargefamilies">Breaking down large families</h2> <p> Large families that would be too complex to analyse are recursively broken down with <a href="http://www.ncbi.nlm.nih.gov/pubmed/12424131">QuickTree</a>. The current limits are 1,500 for <a href="homology_method.html">protein trees</a> and 400 for <a href="ncRNA_methods.html">ncRNA trees</a>. This happens dynamically based on the gene count of each family. </p> <p> The process generates a set of sub-families, each smaller than the required size, and a reconciled binary tree that links them. We apply our <a href="homology_types.html">standard homology inference</a>, but only for paralogues as those super trees generally capture ancient duplication events. We call these paralogues <em>Ancient paralogues</em> in the <a href="http://www.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?g=ENSG00000138759">Paralogues table</a> of the web site, and <code>other_paralog</code> in the database and in BioMart. </p> <h2 id="panthersubfamilies">Panther sub-families in the HMM library</h2> <p> We classify the protein-coding genes into families using a <a href="hmm_lib.html">library of HMMs</a> based on <a href="http://www.pantherdb.org/">Panther</a>. Following an assessment of family sizes and quality across all eukaryotes, we have decided to use the Panther sub-families instead of the families in some cases. In those cases, the HMM library only contains the sub-families (as if they were families), and not their family. </p> <p> For each of these broken-down Panther families, we create a super tree to record the fact that there is a known homology between the sub-families. However, we don't compute the topology of this super tree so it remains flat (up to 300 nodes). Therefore, it is not reconciled with the species tree and lacks speciation / duplication annotations. To infer orthologies between sub-families, we compare them in a pairwise fashion. If a pair of sub-families share at least one species, we record all paralogues between them as <em>Ancient paralogues</em> / <code>other_paralog</code> like above. Otherwise, we record every pair of genes between them as orthologues, following our standard <a href="homology_types.html">naming rule</a> of the relationship cardinality. </p> </div></div> </div> <div id="footer"> <div class="column-wrapper"> <div class="column-two left"> <p> Ensembl Metazoa release 60 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" style="white-space:nowrap">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI</span> </p> </div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div id="fat-footer"> <div class="column-four left"> <h3>About Us</h3> <p><a href="/info/about/">About us</a></p> <p><a href="/info/about/contact/">Contact us</a></p> <p><a href="/info/about/publications.html">Citing Ensembl Genomes</a></p> <p><a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice">Privacy policy</a></p> <p><a href="/info/about/legal/">Disclaimer</a></p> </div> <div class="column-four left"> <h3>Get help</h3> 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