CINXE.COM

<!DOCTYPE html> <html class="client-nojs vector-feature-language-in-header-enabled vector-feature-language-in-main-page-header-disabled vector-feature-sticky-header-disabled vector-feature-page-tools-pinned-disabled vector-feature-toc-pinned-clientpref-1 vector-feature-main-menu-pinned-disabled vector-feature-limited-width-clientpref-1 vector-feature-limited-width-content-disabled vector-feature-custom-font-size-clientpref-1 vector-feature-appearance-pinned-clientpref-1 vector-feature-night-mode-enabled skin-theme-clientpref-day vector-toc-not-available" lang="en" dir="ltr"> <head> <meta charset="UTF-8"> <title>View source for Phylogenomics - Wikipedia</title> <script>(function(){var className="client-js vector-feature-language-in-header-enabled vector-feature-language-in-main-page-header-disabled vector-feature-sticky-header-disabled vector-feature-page-tools-pinned-disabled vector-feature-toc-pinned-clientpref-1 vector-feature-main-menu-pinned-disabled vector-feature-limited-width-clientpref-1 vector-feature-limited-width-content-disabled vector-feature-custom-font-size-clientpref-1 vector-feature-appearance-pinned-clientpref-1 vector-feature-night-mode-enabled skin-theme-clientpref-day vector-toc-not-available";var cookie=document.cookie.match(/(?:^|; )enwikimwclientpreferences=([^;]+)/);if(cookie){cookie[1].split('%2C').forEach(function(pref){className=className.replace(new RegExp('(^| )'+pref.replace(/-clientpref-\w+$|[^\w-]+/g,'')+'-clientpref-\\w+( |$)'),'$1'+pref+'$2');});}document.documentElement.className=className;}());RLCONF={"wgBreakFrames":true,"wgSeparatorTransformTable":["",""],"wgDigitTransformTable":["",""],"wgDefaultDateFormat": "dmy","wgMonthNames":["","January","February","March","April","May","June","July","August","September","October","November","December"],"wgRequestId":"0f40357e-8cf8-44e1-b00a-d3c79c2acb80","wgCanonicalNamespace":"","wgCanonicalSpecialPageName":false,"wgNamespaceNumber":0,"wgPageName":"Phylogenomics","wgTitle":"Phylogenomics","wgCurRevisionId":1188168088,"wgRevisionId":0,"wgArticleId":3485068,"wgIsArticle":false,"wgIsRedirect":false,"wgAction":"edit","wgUserName":null,"wgUserGroups":["*"],"wgCategories":[],"wgPageViewLanguage":"en","wgPageContentLanguage":"en","wgPageContentModel":"wikitext","wgRelevantPageName":"Phylogenomics","wgRelevantArticleId":3485068,"wgIsProbablyEditable":true,"wgRelevantPageIsProbablyEditable":true,"wgRestrictionEdit":[],"wgRestrictionMove":[],"wgNoticeProject":"wikipedia","wgCiteReferencePreviewsActive":false,"wgFlaggedRevsParams":{"tags":{"status":{"levels":1}}},"wgMediaViewerOnClick":true,"wgMediaViewerEnabledByDefault":true,"wgPopupsFlags":0, "wgVisualEditor":{"pageLanguageCode":"en","pageLanguageDir":"ltr","pageVariantFallbacks":"en"},"wgMFDisplayWikibaseDescriptions":{"search":true,"watchlist":true,"tagline":false,"nearby":true},"wgWMESchemaEditAttemptStepOversample":false,"wgWMEPageLength":10000,"wgRelatedArticlesCompat":[],"wgCentralAuthMobileDomain":false,"wgEditSubmitButtonLabelPublish":true,"wgULSPosition":"interlanguage","wgULSisCompactLinksEnabled":false,"wgVector2022LanguageInHeader":true,"wgULSisLanguageSelectorEmpty":false,"wgCheckUserClientHintsHeadersJsApi":["brands","architecture","bitness","fullVersionList","mobile","model","platform","platformVersion"],"GEHomepageSuggestedEditsEnableTopics":true,"wgGETopicsMatchModeEnabled":false,"wgGEStructuredTaskRejectionReasonTextInputEnabled":false,"wgGELevelingUpEnabledForUser":false};RLSTATE={"ext.globalCssJs.user.styles":"ready","site.styles":"ready","user.styles":"ready","ext.globalCssJs.user":"ready","user":"ready","user.options":"loading", "skins.vector.search.codex.styles":"ready","skins.vector.styles":"ready","skins.vector.icons":"ready","jquery.makeCollapsible.styles":"ready","ext.charinsert.styles":"ready","ext.wikimediamessages.styles":"ready","ext.visualEditor.desktopArticleTarget.noscript":"ready","ext.uls.interlanguage":"ready","ext.wikimediaBadges":"ready"};RLPAGEMODULES=["mediawiki.action.edit.collapsibleFooter","site","mediawiki.page.ready","jquery.makeCollapsible","skins.vector.js","ext.centralNotice.geoIP","ext.charinsert","ext.gadget.ReferenceTooltips","ext.gadget.charinsert","ext.gadget.extra-toolbar-buttons","ext.gadget.refToolbar","ext.gadget.switcher","ext.urlShortener.toolbar","ext.centralauth.centralautologin","mmv.bootstrap","ext.popups","ext.visualEditor.desktopArticleTarget.init","ext.visualEditor.targetLoader","ext.echo.centralauth","ext.eventLogging","ext.wikimediaEvents","ext.navigationTiming","ext.uls.interface","ext.cx.eventlogging.campaigns","ext.checkUser.clientHints", "ext.growthExperiments.SuggestedEditSession","wikibase.sidebar.tracking"];</script> <script>(RLQ=window.RLQ||[]).push(function(){mw.loader.impl(function(){return["user.options@12s5i",function($,jQuery,require,module){mw.user.tokens.set({"patrolToken":"+\\","watchToken":"+\\","csrfToken":"+\\"}); }];});});</script> <link rel="stylesheet" href="/w/load.php?lang=en&modules=ext.charinsert.styles%7Cext.uls.interlanguage%7Cext.visualEditor.desktopArticleTarget.noscript%7Cext.wikimediaBadges%7Cext.wikimediamessages.styles%7Cjquery.makeCollapsible.styles%7Cskins.vector.icons%2Cstyles%7Cskins.vector.search.codex.styles&only=styles&skin=vector-2022"> <script async="" src="/w/load.php?lang=en&modules=startup&only=scripts&raw=1&skin=vector-2022"></script> <meta name="ResourceLoaderDynamicStyles" content=""> <link rel="stylesheet" href="/w/load.php?lang=en&modules=site.styles&only=styles&skin=vector-2022"> <meta name="generator" content="MediaWiki 1.44.0-wmf.4"> <meta name="referrer" content="origin"> <meta name="referrer" content="origin-when-cross-origin"> <meta name="robots" content="noindex,nofollow,max-image-preview:standard"> <meta name="format-detection" content="telephone=no"> <meta name="viewport" content="width=1120"> <meta property="og:title" content="View source for Phylogenomics - Wikipedia"> <meta property="og:type" content="website"> <link rel="preconnect" href="//upload.wikimedia.org"> <link rel="alternate" media="only screen and (max-width: 640px)" href="//en.m.wikipedia.org/wiki/Phylogenomics"> <link rel="alternate" type="application/x-wiki" title="Edit this page" href="/w/index.php?title=Phylogenomics&action=edit"> <link rel="apple-touch-icon" href="/static/apple-touch/wikipedia.png"> <link rel="icon" href="/static/favicon/wikipedia.ico"> <link rel="search" type="application/opensearchdescription+xml" href="/w/rest.php/v1/search" title="Wikipedia (en)"> <link rel="EditURI" type="application/rsd+xml" href="//en.wikipedia.org/w/api.php?action=rsd"> <link rel="canonical" href="https://en.wikipedia.org/wiki/Phylogenomics"> <link rel="license" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en"> <link rel="alternate" type="application/atom+xml" title="Wikipedia Atom feed" href="/w/index.php?title=Special:RecentChanges&feed=atom"> <link rel="dns-prefetch" href="//login.wikimedia.org"> </head> <body class="skin--responsive skin-vector skin-vector-search-vue mediawiki ltr sitedir-ltr mw-hide-empty-elt ns-0 ns-subject mw-editable page-Phylogenomics rootpage-Phylogenomics skin-vector-2022 action-edit"><a class="mw-jump-link" href="#bodyContent">Jump to content</a> <div class="vector-header-container"> <header class="vector-header mw-header"> <div class="vector-header-start"> <nav class="vector-main-menu-landmark" aria-label="Site"> <div id="vector-main-menu-dropdown" class="vector-dropdown vector-main-menu-dropdown vector-button-flush-left vector-button-flush-right" > <input type="checkbox" id="vector-main-menu-dropdown-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-main-menu-dropdown" class="vector-dropdown-checkbox " aria-label="Main menu" > <label id="vector-main-menu-dropdown-label" for="vector-main-menu-dropdown-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only " aria-hidden="true" ><span class="vector-icon mw-ui-icon-menu mw-ui-icon-wikimedia-menu"></span> <span class="vector-dropdown-label-text">Main menu</span> </label> <div class="vector-dropdown-content"> <div id="vector-main-menu-unpinned-container" class="vector-unpinned-container"> <div id="vector-main-menu" class="vector-main-menu vector-pinnable-element"> <div class="vector-pinnable-header vector-main-menu-pinnable-header vector-pinnable-header-unpinned" data-feature-name="main-menu-pinned" data-pinnable-element-id="vector-main-menu" data-pinned-container-id="vector-main-menu-pinned-container" data-unpinned-container-id="vector-main-menu-unpinned-container" > <div class="vector-pinnable-header-label">Main menu</div> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-pin-button" data-event-name="pinnable-header.vector-main-menu.pin">move to sidebar</button> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-unpin-button" data-event-name="pinnable-header.vector-main-menu.unpin">hide</button> </div> <div id="p-navigation" class="vector-menu mw-portlet mw-portlet-navigation" > <div class="vector-menu-heading"> Navigation </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="n-mainpage-description" class="mw-list-item"><a href="/wiki/Main_Page" title="Visit the main page [z]" accesskey="z"><span>Main page</span></a></li><li id="n-contents" class="mw-list-item"><a href="/wiki/Wikipedia:Contents" title="Guides to browsing Wikipedia"><span>Contents</span></a></li><li id="n-currentevents" class="mw-list-item"><a href="/wiki/Portal:Current_events" title="Articles related to current events"><span>Current events</span></a></li><li id="n-randompage" class="mw-list-item"><a href="/wiki/Special:Random" title="Visit a randomly selected article [x]" accesskey="x"><span>Random article</span></a></li><li id="n-aboutsite" class="mw-list-item"><a href="/wiki/Wikipedia:About" title="Learn about Wikipedia and how it works"><span>About Wikipedia</span></a></li><li id="n-contactpage" class="mw-list-item"><a href="//en.wikipedia.org/wiki/Wikipedia:Contact_us" title="How to contact Wikipedia"><span>Contact us</span></a></li> </ul> </div> </div> <div id="p-interaction" class="vector-menu mw-portlet mw-portlet-interaction" > <div class="vector-menu-heading"> Contribute </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="n-help" class="mw-list-item"><a href="/wiki/Help:Contents" title="Guidance on how to use and edit Wikipedia"><span>Help</span></a></li><li id="n-introduction" class="mw-list-item"><a href="/wiki/Help:Introduction" title="Learn how to edit Wikipedia"><span>Learn to edit</span></a></li><li id="n-portal" class="mw-list-item"><a href="/wiki/Wikipedia:Community_portal" title="The hub for editors"><span>Community portal</span></a></li><li id="n-recentchanges" class="mw-list-item"><a href="/wiki/Special:RecentChanges" title="A list of recent changes to Wikipedia [r]" accesskey="r"><span>Recent changes</span></a></li><li id="n-upload" class="mw-list-item"><a href="/wiki/Wikipedia:File_upload_wizard" title="Add images or other media for use on Wikipedia"><span>Upload file</span></a></li> </ul> </div> </div> </div> </div> </div> </div> </nav> <a href="/wiki/Main_Page" class="mw-logo"> <img class="mw-logo-icon" src="/static/images/icons/wikipedia.png" alt="" aria-hidden="true" height="50" width="50"> <span class="mw-logo-container skin-invert"> <img class="mw-logo-wordmark" alt="Wikipedia" src="/static/images/mobile/copyright/wikipedia-wordmark-en.svg" style="width: 7.5em; height: 1.125em;"> <img class="mw-logo-tagline" alt="The Free Encyclopedia" src="/static/images/mobile/copyright/wikipedia-tagline-en.svg" width="117" height="13" style="width: 7.3125em; height: 0.8125em;"> </span> </a> </div> <div class="vector-header-end"> <div id="p-search" role="search" class="vector-search-box-vue vector-search-box-collapses vector-search-box-show-thumbnail vector-search-box-auto-expand-width vector-search-box"> <a href="/wiki/Special:Search" class="cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only search-toggle" title="Search Wikipedia [f]" accesskey="f"><span class="vector-icon mw-ui-icon-search mw-ui-icon-wikimedia-search"></span> <span>Search</span> </a> <div class="vector-typeahead-search-container"> <div class="cdx-typeahead-search cdx-typeahead-search--show-thumbnail cdx-typeahead-search--auto-expand-width"> <form action="/w/index.php" id="searchform" class="cdx-search-input cdx-search-input--has-end-button"> <div id="simpleSearch" class="cdx-search-input__input-wrapper" data-search-loc="header-moved"> <div class="cdx-text-input cdx-text-input--has-start-icon"> <input class="cdx-text-input__input" type="search" name="search" placeholder="Search Wikipedia" aria-label="Search Wikipedia" autocapitalize="sentences" title="Search Wikipedia [f]" accesskey="f" id="searchInput" > <span class="cdx-text-input__icon cdx-text-input__start-icon"></span> </div> <input type="hidden" name="title" value="Special:Search"> </div> <button class="cdx-button cdx-search-input__end-button">Search</button> </form> </div> </div> </div> <nav class="vector-user-links vector-user-links-wide" aria-label="Personal tools"> <div class="vector-user-links-main"> <div id="p-vector-user-menu-preferences" class="vector-menu mw-portlet emptyPortlet" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> </ul> </div> </div> <div id="p-vector-user-menu-userpage" class="vector-menu mw-portlet emptyPortlet" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> </ul> </div> </div> <nav class="vector-appearance-landmark" aria-label="Appearance"> <div id="vector-appearance-dropdown" class="vector-dropdown " title="Change the appearance of the page's font size, width, and color" > <input type="checkbox" id="vector-appearance-dropdown-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-appearance-dropdown" class="vector-dropdown-checkbox " aria-label="Appearance" > <label id="vector-appearance-dropdown-label" for="vector-appearance-dropdown-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only " aria-hidden="true" ><span class="vector-icon mw-ui-icon-appearance mw-ui-icon-wikimedia-appearance"></span> <span class="vector-dropdown-label-text">Appearance</span> </label> <div class="vector-dropdown-content"> <div id="vector-appearance-unpinned-container" class="vector-unpinned-container"> </div> </div> </div> </nav> <div id="p-vector-user-menu-notifications" class="vector-menu mw-portlet emptyPortlet" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> </ul> </div> </div> <div id="p-vector-user-menu-overflow" class="vector-menu mw-portlet" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="pt-sitesupport-2" class="user-links-collapsible-item mw-list-item user-links-collapsible-item"><a data-mw="interface" href="https://donate.wikimedia.org/wiki/Special:FundraiserRedirector?utm_source=donate&utm_medium=sidebar&utm_campaign=C13_en.wikipedia.org&uselang=en" class=""><span>Donate</span></a> </li> <li id="pt-createaccount-2" class="user-links-collapsible-item mw-list-item user-links-collapsible-item"><a data-mw="interface" href="/w/index.php?title=Special:CreateAccount&returnto=Phylogenomics&returntoquery=action%3Dedit" title="You are encouraged to create an account and log in; however, it is not mandatory" class=""><span>Create account</span></a> </li> <li id="pt-login-2" class="user-links-collapsible-item mw-list-item user-links-collapsible-item"><a data-mw="interface" href="/w/index.php?title=Special:UserLogin&returnto=Phylogenomics&returntoquery=action%3Dedit" title="You're encouraged to log in; however, it's not mandatory. [o]" accesskey="o" class=""><span>Log in</span></a> </li> </ul> </div> </div> </div> <div id="vector-user-links-dropdown" class="vector-dropdown vector-user-menu vector-button-flush-right vector-user-menu-logged-out" title="Log in and more options" > <input type="checkbox" id="vector-user-links-dropdown-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-user-links-dropdown" class="vector-dropdown-checkbox " aria-label="Personal tools" > <label id="vector-user-links-dropdown-label" for="vector-user-links-dropdown-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only " aria-hidden="true" ><span class="vector-icon mw-ui-icon-ellipsis mw-ui-icon-wikimedia-ellipsis"></span> <span class="vector-dropdown-label-text">Personal tools</span> </label> <div class="vector-dropdown-content"> <div id="p-personal" class="vector-menu mw-portlet mw-portlet-personal user-links-collapsible-item" title="User menu" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="pt-sitesupport" class="user-links-collapsible-item mw-list-item"><a href="https://donate.wikimedia.org/wiki/Special:FundraiserRedirector?utm_source=donate&utm_medium=sidebar&utm_campaign=C13_en.wikipedia.org&uselang=en"><span>Donate</span></a></li><li id="pt-createaccount" class="user-links-collapsible-item mw-list-item"><a href="/w/index.php?title=Special:CreateAccount&returnto=Phylogenomics&returntoquery=action%3Dedit" title="You are encouraged to create an account and log in; however, it is not mandatory"><span class="vector-icon mw-ui-icon-userAdd mw-ui-icon-wikimedia-userAdd"></span> <span>Create account</span></a></li><li id="pt-login" class="user-links-collapsible-item mw-list-item"><a href="/w/index.php?title=Special:UserLogin&returnto=Phylogenomics&returntoquery=action%3Dedit" title="You're encouraged to log in; however, it's not mandatory. [o]" accesskey="o"><span class="vector-icon mw-ui-icon-logIn mw-ui-icon-wikimedia-logIn"></span> <span>Log in</span></a></li> </ul> </div> </div> <div id="p-user-menu-anon-editor" class="vector-menu mw-portlet mw-portlet-user-menu-anon-editor" > <div class="vector-menu-heading"> Pages for logged out editors <a href="/wiki/Help:Introduction" aria-label="Learn more about editing"><span>learn more</span></a> </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="pt-anoncontribs" class="mw-list-item"><a href="/wiki/Special:MyContributions" title="A list of edits made from this IP address [y]" accesskey="y"><span>Contributions</span></a></li><li id="pt-anontalk" class="mw-list-item"><a href="/wiki/Special:MyTalk" title="Discussion about edits from this IP address [n]" accesskey="n"><span>Talk</span></a></li> </ul> </div> </div> </div> </div> </nav> </div> </header> </div> <div class="mw-page-container"> <div class="mw-page-container-inner"> <div class="vector-sitenotice-container"> <div id="siteNotice"></div> </div> <div class="vector-column-start"> <div class="vector-main-menu-container"> <div id="mw-navigation"> <nav id="mw-panel" class="vector-main-menu-landmark" aria-label="Site"> <div id="vector-main-menu-pinned-container" class="vector-pinned-container"> </div> </nav> </div> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header vector-page-titlebar"> <h1 id="firstHeading" class="firstHeading mw-first-heading">View source for Phylogenomics</h1> <div id="p-lang-btn" class="vector-dropdown mw-portlet mw-portlet-lang" > <input type="checkbox" id="p-lang-btn-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-lang-btn" class="vector-dropdown-checkbox mw-interlanguage-selector" aria-label="This article exist only in this language. Add the article for other languages" > <label id="p-lang-btn-label" for="p-lang-btn-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--action-progressive mw-portlet-lang-heading-0" aria-hidden="true" ><span class="vector-icon mw-ui-icon-language-progressive mw-ui-icon-wikimedia-language-progressive"></span> <span class="vector-dropdown-label-text">Add languages</span> </label> <div class="vector-dropdown-content"> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> </ul> <div class="after-portlet after-portlet-lang"><span class="uls-after-portlet-link"></span></div> </div> </div> </div> </header> <div class="vector-page-toolbar"> <div class="vector-page-toolbar-container"> <div id="left-navigation"> <nav aria-label="Namespaces"> <div id="p-associated-pages" class="vector-menu vector-menu-tabs mw-portlet mw-portlet-associated-pages" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="ca-nstab-main" class="selected vector-tab-noicon mw-list-item"><a href="/wiki/Phylogenomics" title="View the content page [c]" accesskey="c"><span>Article</span></a></li><li id="ca-talk" class="vector-tab-noicon mw-list-item"><a href="/wiki/Talk:Phylogenomics" rel="discussion" title="Discuss improvements to the content page [t]" accesskey="t"><span>Talk</span></a></li> </ul> </div> </div> <div id="vector-variants-dropdown" class="vector-dropdown emptyPortlet" > <input type="checkbox" id="vector-variants-dropdown-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-variants-dropdown" class="vector-dropdown-checkbox " aria-label="Change language variant" > <label id="vector-variants-dropdown-label" for="vector-variants-dropdown-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet" aria-hidden="true" ><span class="vector-dropdown-label-text">English</span> </label> <div class="vector-dropdown-content"> <div id="p-variants" class="vector-menu mw-portlet mw-portlet-variants emptyPortlet" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> </ul> </div> </div> </div> </div> </nav> </div> <div id="right-navigation" class="vector-collapsible"> <nav aria-label="Views"> <div id="p-views" class="vector-menu vector-menu-tabs mw-portlet mw-portlet-views" > <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="ca-view" class="vector-tab-noicon mw-list-item"><a href="/wiki/Phylogenomics"><span>Read</span></a></li><li id="ca-edit" class="selected vector-tab-noicon mw-list-item"><a href="/w/index.php?title=Phylogenomics&action=edit" title="Edit this page"><span>Edit</span></a></li><li id="ca-history" class="vector-tab-noicon mw-list-item"><a href="/w/index.php?title=Phylogenomics&action=history" title="Past revisions of this page [h]" accesskey="h"><span>View history</span></a></li> </ul> </div> </div> </nav> <nav class="vector-page-tools-landmark" aria-label="Page tools"> <div id="vector-page-tools-dropdown" class="vector-dropdown vector-page-tools-dropdown" > <input type="checkbox" id="vector-page-tools-dropdown-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-page-tools-dropdown" class="vector-dropdown-checkbox " aria-label="Tools" > <label id="vector-page-tools-dropdown-label" for="vector-page-tools-dropdown-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet" aria-hidden="true" ><span class="vector-dropdown-label-text">Tools</span> </label> <div class="vector-dropdown-content"> <div id="vector-page-tools-unpinned-container" class="vector-unpinned-container"> <div id="vector-page-tools" class="vector-page-tools vector-pinnable-element"> <div class="vector-pinnable-header vector-page-tools-pinnable-header vector-pinnable-header-unpinned" data-feature-name="page-tools-pinned" data-pinnable-element-id="vector-page-tools" data-pinned-container-id="vector-page-tools-pinned-container" data-unpinned-container-id="vector-page-tools-unpinned-container" > <div class="vector-pinnable-header-label">Tools</div> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-pin-button" data-event-name="pinnable-header.vector-page-tools.pin">move to sidebar</button> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-unpin-button" data-event-name="pinnable-header.vector-page-tools.unpin">hide</button> </div> <div id="p-cactions" class="vector-menu mw-portlet mw-portlet-cactions emptyPortlet vector-has-collapsible-items" title="More options" > <div class="vector-menu-heading"> Actions </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="ca-more-view" class="vector-more-collapsible-item mw-list-item"><a href="/wiki/Phylogenomics"><span>Read</span></a></li><li id="ca-more-edit" class="selected vector-more-collapsible-item mw-list-item"><a href="/w/index.php?title=Phylogenomics&action=edit" title="Edit this page [e]" accesskey="e"><span>Edit</span></a></li><li id="ca-more-history" class="vector-more-collapsible-item mw-list-item"><a href="/w/index.php?title=Phylogenomics&action=history"><span>View history</span></a></li> </ul> </div> </div> <div id="p-tb" class="vector-menu mw-portlet mw-portlet-tb" > <div class="vector-menu-heading"> General </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="t-whatlinkshere" class="mw-list-item"><a href="/wiki/Special:WhatLinksHere/Phylogenomics" title="List of all English Wikipedia pages containing links to this page [j]" accesskey="j"><span>What links here</span></a></li><li id="t-recentchangeslinked" class="mw-list-item"><a href="/wiki/Special:RecentChangesLinked/Phylogenomics" rel="nofollow" title="Recent changes in pages linked from this page [k]" accesskey="k"><span>Related changes</span></a></li><li id="t-upload" class="mw-list-item"><a href="/wiki/Wikipedia:File_Upload_Wizard" title="Upload files [u]" accesskey="u"><span>Upload file</span></a></li><li id="t-specialpages" class="mw-list-item"><a href="/wiki/Special:SpecialPages" title="A list of all special pages [q]" accesskey="q"><span>Special pages</span></a></li><li id="t-info" class="mw-list-item"><a href="/w/index.php?title=Phylogenomics&action=info" title="More information about this page"><span>Page information</span></a></li><li id="t-urlshortener" class="mw-list-item"><a href="/w/index.php?title=Special:UrlShortener&url=https%3A%2F%2Fen.wikipedia.org%2Fw%2Findex.php%3Ftitle%3DPhylogenomics%26action%3Dedit"><span>Get shortened URL</span></a></li><li id="t-urlshortener-qrcode" class="mw-list-item"><a href="/w/index.php?title=Special:QrCode&url=https%3A%2F%2Fen.wikipedia.org%2Fw%2Findex.php%3Ftitle%3DPhylogenomics%26action%3Dedit"><span>Download QR code</span></a></li> </ul> </div> </div> <div id="p-wikibase-otherprojects" class="vector-menu mw-portlet mw-portlet-wikibase-otherprojects" > <div class="vector-menu-heading"> In other projects </div> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li id="t-wikibase" class="wb-otherproject-link wb-otherproject-wikibase-dataitem mw-list-item"><a href="https://www.wikidata.org/wiki/Special:EntityPage/Q3381973" title="Structured data on this page hosted by Wikidata [g]" accesskey="g"><span>Wikidata item</span></a></li> </ul> </div> </div> </div> </div> </div> </div> </nav> </div> </div> </div> <div class="vector-column-end"> <div class="vector-sticky-pinned-container"> <nav class="vector-page-tools-landmark" aria-label="Page tools"> <div id="vector-page-tools-pinned-container" class="vector-pinned-container"> </div> </nav> <nav class="vector-appearance-landmark" aria-label="Appearance"> <div id="vector-appearance-pinned-container" class="vector-pinned-container"> <div id="vector-appearance" class="vector-appearance vector-pinnable-element"> <div class="vector-pinnable-header vector-appearance-pinnable-header vector-pinnable-header-pinned" data-feature-name="appearance-pinned" data-pinnable-element-id="vector-appearance" data-pinned-container-id="vector-appearance-pinned-container" data-unpinned-container-id="vector-appearance-unpinned-container" > <div class="vector-pinnable-header-label">Appearance</div> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-pin-button" data-event-name="pinnable-header.vector-appearance.pin">move to sidebar</button> <button class="vector-pinnable-header-toggle-button vector-pinnable-header-unpin-button" data-event-name="pinnable-header.vector-appearance.unpin">hide</button> </div> </div> </div> </nav> </div> </div> <div id="bodyContent" class="vector-body" aria-labelledby="firstHeading" data-mw-ve-target-container> <div class="vector-body-before-content"> <div class="mw-indicators"> </div> </div> <div id="contentSub"><div id="mw-content-subtitle">← <a href="/wiki/Phylogenomics" title="Phylogenomics">Phylogenomics</a></div></div> <div id="mw-content-text" class="mw-body-content"><p>You do not have permission to edit this page, for the following reasons: </p> <ul class="permissions-errors"><li class="mw-permissionerror-blockedtext"> <div id="mw-blocked-text" style="border: 1px solid #AAA; background-color: var(--background-color-warning-subtle, ivory); color: inherit; padding: 1.5em; width: 100%; box-sizing: border-box;"> <div style="text-align: center;"><span style="font-size: 26px;"><span typeof="mw:File"><a href="/wiki/File:Stop_hand_nuvola.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/50px-Stop_hand_nuvola.svg.png" decoding="async" width="50" height="50" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/75px-Stop_hand_nuvola.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/100px-Stop_hand_nuvola.svg.png 2x" data-file-width="240" data-file-height="240" /></a></span><b> This IP address has been <a href="/wiki/Wikipedia:Blocking_policy" title="Wikipedia:Blocking policy">blocked</a> from <i>editing</i> Wikipedia.</b></span><br /><span style="font-size: 18px;">This does not affect your ability to <i>read</i> Wikipedia pages.</span></div><div class="paragraphbreak" style="margin-top:0.5em"></div><b>Most people who see this message have done nothing wrong.</b> Some kinds of blocks restrict editing from specific service providers or telecom companies in response to recent abuse or vandalism, and can sometimes affect other users who are unrelated to that abuse. Review the information below for assistance if you do not believe that you have done anything wrong.<div class="paragraphbreak" style="margin-top:0.5em"></div> <p>The IP address or range 8.222.128.0/17 has been <a href="/wiki/Wikipedia:Blocking_policy" title="Wikipedia:Blocking policy">blocked</a> by <a href="/wiki/User:L235" title="User:L235">‪L235‬</a> for the following reason(s): </p> <div style="padding:10px; background:var(--background-color-base, white); color:inherit; border:1px #666 solid;"> <div class="user-block colocation-webhost" style="margin-bottom: 0.5em; background-color: #ffefd5; border: 1px solid #AAA; padding: 0.7em;"> <figure class="mw-halign-left" typeof="mw:File"><span><img src="//upload.wikimedia.org/wikipedia/commons/thumb/5/53/Server-multiple.svg/40px-Server-multiple.svg.png" decoding="async" width="40" height="57" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/5/53/Server-multiple.svg/60px-Server-multiple.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/5/53/Server-multiple.svg/80px-Server-multiple.svg.png 2x" data-file-width="744" data-file-height="1052" /></span><figcaption></figcaption></figure><b>The <a href="/wiki/IP_address" title="IP address">IP address</a> that you are currently using has been blocked because it is believed to be a <a href="/wiki/Web_hosting_service" title="Web hosting service">web host provider</a> or <a href="/wiki/Colocation_centre" title="Colocation centre">colocation provider</a>.</b> To prevent abuse, <a href="/wiki/Wikipedia:Open_proxies" title="Wikipedia:Open proxies">web hosts and colocation providers may be blocked</a> from editing Wikipedia. <div style="border-top: 1px solid #AAA; clear: both">You will not be able to edit Wikipedia using a web host or colocation provider because it hides your IP address, much like a <a href="/wiki/Wikipedia:Open_proxies" title="Wikipedia:Open proxies">proxy</a> or <a href="/wiki/Virtual_private_network" title="Virtual private network">VPN</a>. <p><b>We recommend that you attempt to use another connection to edit.</b> For example, if you use a proxy or VPN to connect to the internet, turn it off when editing Wikipedia. If you edit using a mobile connection, try using a Wi-Fi connection, and vice versa. If you are using a corporate internet connection, switch to a different Wi-Fi network. If you have a Wikipedia account, please log in. </p><p>If you do not have any other way to edit Wikipedia, you will need to <a href="/wiki/Wikipedia:IP_block_exemption#Requesting_and_granting_exemption" title="Wikipedia:IP block exemption">request an IP block exemption</a>. </p> <style data-mw-deduplicate="TemplateStyles:r1214851843">.mw-parser-output .hidden-begin{box-sizing:border-box;width:100%;padding:5px;border:none;font-size:95%}.mw-parser-output .hidden-title{font-weight:bold;line-height:1.6;text-align:left}.mw-parser-output .hidden-content{text-align:left}@media all and (max-width:500px){.mw-parser-output .hidden-begin{width:auto!important;clear:none!important;float:none!important}}</style><div class="hidden-begin mw-collapsible mw-collapsed" style=""><div class="hidden-title skin-nightmode-reset-color" style="text-align:center;">How to appeal if you are confident that your connection does not use a colocation provider's IP address:</div><div class="hidden-content mw-collapsible-content" style=""> If you are confident that you are not using a web host, you may <a href="/wiki/Wikipedia:Appealing_a_block" title="Wikipedia:Appealing a block">appeal this block</a> by adding the following text on your <a href="/wiki/Help:Talk_pages" title="Help:Talk pages">talk page</a>: <code>{{<a href="/wiki/Template:Unblock" title="Template:Unblock">unblock</a>|reason=Caught by a colocation web host block but this host or IP is not a web host. My IP address is _______. <i>Place any further information here.</i> ~~~~}}</code>. <b>You must fill in the blank with your IP address for this block to be investigated.</b> Your IP address can be determined <span class="plainlinks"><b><a class="external text" href="https://en.wikipedia.org/wiki/Wikipedia:Get_my_IP_address?withJS=MediaWiki:Get-my-ip.js">here</a></b></span>. Alternatively, if you wish to keep your IP address private you can use the <a href="/wiki/Wikipedia:Unblock_Ticket_Request_System" title="Wikipedia:Unblock Ticket Request System">unblock ticket request system</a>. There are several reasons you might be editing using the IP address of a web host or colocation provider (such as if you are using VPN software or a business network); please use this method of appeal only if you think your IP address is in fact not a web host or colocation provider.</div></div> <p><span class="sysop-show" style="font-size: 85%;"><span style="border:#707070 solid 1px;background-color:#ffe0e0;padding:2px"><b>Administrators:</b></span> The <a href="/wiki/Wikipedia:IP_block_exemption" title="Wikipedia:IP block exemption">IP block exemption</a> user right should only be applied to allow users to edit using web host in exceptional circumstances, and requests should usually be directed to the functionaries team via email. If you intend to give the IPBE user right, a <a href="/wiki/Wikipedia:CheckUser" title="Wikipedia:CheckUser">CheckUser</a> needs to take a look at the account. This can be requested most easily at <a href="/wiki/Wikipedia:SPI#Quick_CheckUser_requests" class="mw-redirect" title="Wikipedia:SPI">SPI Quick Checkuser Requests</a>. <b>Unblocking</b> an IP or IP range with this template <b>is highly discouraged</b> without at least contacting the blocking administrator.</span> </p> </div></div> </div> <p>This block will expire on 18:23, 24 August 2026. Your current IP address is 8.222.208.146. </p> <div class="paragraphbreak" style="margin-top:0.5em"></div><div style="font-size: 16px;"> <p>Even when blocked, you will <i>usually</i> still be able to edit your <a href="/wiki/Special:MyTalk" title="Special:MyTalk">user talk page</a>, as well as <a href="/wiki/Wikipedia:Emailing_users" title="Wikipedia:Emailing users">email</a> administrators and other editors. </p> </div> <div class="paragraphbreak" style="margin-top:0.5em"></div><div style="font-size: 16px;"> <p>For information on how to proceed, please read the <b><a href="/wiki/Wikipedia:Appealing_a_block#Common_questions" title="Wikipedia:Appealing a block">FAQ for blocked users</a></b> and the <a href="/wiki/Wikipedia:Appealing_a_block" title="Wikipedia:Appealing a block">guideline on block appeals</a>. The <a href="/wiki/Wikipedia:Guide_to_appealing_blocks" title="Wikipedia:Guide to appealing blocks">guide to appealing blocks</a> may also be helpful. </p> </div> <p>Other useful links: <a href="/wiki/Wikipedia:Blocking_policy" title="Wikipedia:Blocking policy">Blocking policy</a> · <a href="/wiki/Help:I_have_been_blocked" title="Help:I have been blocked">Help:I have been blocked</a> </p> </div></li><li class="mw-permissionerror-globalblocking-blockedtext-range"> <div id="mw-blocked-text" style="border: 1px solid #AAA; background-color: var(--background-color-warning-subtle, ivory); color: inherit; padding: 1.5em; width: 100%; box-sizing: border-box;"> <div style="text-align: center;"><span style="font-size: 26px;"><span typeof="mw:File"><a href="/wiki/File:Stop_hand_nuvola.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/50px-Stop_hand_nuvola.svg.png" decoding="async" width="50" height="50" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/75px-Stop_hand_nuvola.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/f/f1/Stop_hand_nuvola.svg/100px-Stop_hand_nuvola.svg.png 2x" data-file-width="240" data-file-height="240" /></a></span><b> This IP address range has been <a href="https://meta.wikimedia.org/wiki/Global_blocks" class="extiw" title="m:Global blocks">globally blocked</a>.</b></span><br /><span style="font-size: 18px;">This does not affect your ability to <i>read</i> Wikipedia pages.</span></div><div class="paragraphbreak" style="margin-top:0.5em"></div><b>Most people who see this message have done nothing wrong.</b> Some kinds of blocks restrict editing from specific service providers or telecom companies in response to recent abuse or vandalism, and can sometimes affect other users who are unrelated to that abuse. Review the information below for assistance if you do not believe that you have done anything wrong.<div class="paragraphbreak" style="margin-top:0.5em"></div><div class="paragraphbreak" style="margin-top:0.5em"></div> <p>This block affects editing on all Wikimedia wikis. </p><p>The IP address or range 8.222.128.0/17 has been globally <a href="/wiki/Wikipedia:Blocking_policy" title="Wikipedia:Blocking policy">blocked</a> by <a href="/wiki/User:Jon_Kolbert" title="User:Jon Kolbert">‪Jon Kolbert‬</a> for the following reason(s): </p> <div style="padding:10px; background:var(--background-color-base, white); color:inherit; border:1px #666 solid;"> <p><a href="https://meta.wikimedia.org/wiki/Special:MyLanguage/NOP" class="extiw" title="m:Special:MyLanguage/NOP">Open proxy/Webhost</a>: See the <a href="https://meta.wikimedia.org/wiki/WM:OP/H" class="extiw" title="m:WM:OP/H">help page</a> if you are affected </p> </div> <p>This block will expire on 15:12, 27 August 2028. Your current IP address is 8.222.208.146. </p> <div class="paragraphbreak" style="margin-top:0.5em"></div><div style="font-size: 16px;"> <p>Even while globally blocked, you will <i>usually</i> still be able to edit pages on <a href="https://meta.wikimedia.org/wiki/" class="extiw" title="m:">Meta-Wiki</a>. </p> </div> <div class="paragraphbreak" style="margin-top:0.5em"></div><div style="font-size: 16px;"> <p>If you believe you were blocked by mistake, you can find additional information and instructions in the <a href="https://meta.wikimedia.org/wiki/Special:MyLanguage/No_open_proxies" class="extiw" title="m:Special:MyLanguage/No open proxies">No open proxies</a> global policy. Otherwise, to discuss the block please <a href="https://meta.wikimedia.org/wiki/Steward_requests/Global" class="extiw" title="m:Steward requests/Global">post a request for review on Meta-Wiki</a>. You could also send an email to the <a href="https://meta.wikimedia.org/wiki/Special:MyLanguage/Stewards" class="extiw" title="m:Special:MyLanguage/Stewards">stewards</a> <a href="https://meta.wikimedia.org/wiki/Special:MyLanguage/VRT" class="extiw" title="m:Special:MyLanguage/VRT">VRT</a> queue at <kbd>stewards@wikimedia.org</kbd> including all above details. </p> </div> <p>Other useful links: <a href="https://meta.wikimedia.org/wiki/Global_blocks" class="extiw" title="m:Global blocks">Global blocks</a> · <a href="/wiki/Help:I_have_been_blocked" title="Help:I have been blocked">Help:I have been blocked</a> </p> </div></li></ul><hr /> <div id="viewsourcetext">You can view and copy the source of this page:</div><textarea readonly="" accesskey="," id="wpTextbox1" cols="80" rows="25" style="" class="mw-editfont-monospace" lang="en" dir="ltr" name="wpTextbox1">{{Short description|Intersection of the fields of evolution and genomics}} '''Phylogenomics''' is the intersection of the fields of [[evolution]] and [[genomics]].<ref>[http://www.biomedcentral.com/1471-2148/7/S1/S1 BioMed Central | Fgenerated title -->]</ref> The term has been used in multiple ways to refer to analysis that involves [[genome]] data and evolutionary reconstructions.<ref>{{cite journal | vauthors = Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K | title = Statistics and truth in phylogenomics | journal = Molecular Biology and Evolution | volume = 29 | issue = 2 | pages = 457–472 | date = February 2012 | pmid = 21873298 | pmc = 3258035 | doi = 10.1093/molbev/msr202 }}</ref> It is a group of techniques within the larger fields of [[phylogenetics]] and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes.<ref>{{cite journal | vauthors = Pennisi E | author-link=Elizabeth Pennisi | title = Evolution. Building the tree of life, genome by genome | journal = Science | volume = 320 | issue = 5884 | pages = 1716–1717 | date = June 2008 | pmid = 18583591 | doi = 10.1126/science.320.5884.1716 | s2cid = 206580993 }}</ref> Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: * Prediction of gene function * Establishment and clarification of evolutionary relationships * Gene family evolution * Prediction and retracing [[lateral gene transfer]]. The ultimate goal of phylogenomics is to reconstruct the evolutionary history of species through their genomes. This history is usually inferred from a series of genomes by using a genome evolution model and standard statistical inference methods (e.g. [[Bayesian inference]] or [[maximum likelihood estimation]]). <ref>{{Cite book| vauthors = Simion P, Delsuc F, Phillipe H |title=Phylogenetics in the Genomic Era|year=2020|url=https://hal.inria.fr/PGE|pages=2.1.1–2.1.34|chapter=2.1 To What Extent Current Limits of Phylogenomics Can Be Overcome?}}</ref> ==Prediction of gene function== When [[Jonathan Eisen]] originally coined ''phylogenomics'', it applied to prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. When several genes with similar sequences but differing functions are involved, this method alone is ineffective in determining function. A specific example is presented in the paper "Gastronomic Delights: A movable feast".<ref name="Eisen">{{cite journal | vauthors = Eisen JA, Kaiser D, Myers RM | title = Gastrogenomic delights: a movable feast | journal = Nature Medicine | volume = 3 | issue = 10 | pages = 1076–1078 | date = October 1997 | pmid = 9334711 | pmc = 3155951 | doi = 10.1038/nm1097-1076 }}</ref> Gene predictions based on sequence similarity alone had been used to predict that ''[[Helicobacter pylori]]'' can repair mismatched [[DNA]].<ref name="Tomb">{{cite journal | vauthors = Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC | display-authors = 6 | title = The complete genome sequence of the gastric pathogen Helicobacter pylori | journal = Nature | volume = 388 | issue = 6642 | pages = 539–547 | date = August 1997 | pmid = 9252185 | doi = 10.1038/41483 | doi-access = free }}</ref> This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene family which included many known to be involved in mismatch repair. However, Eisen noted that ''H. pylori'' lacks other genes thought to be essential for this function (specifically, members of the MutL family). Eisen suggested a solution to this apparent discrepancy – phylogenetic trees of genes in the MutS family revealed that the gene found in ''H. pylori'' was not in the same subfamily as those known to be involved in mismatch repair.<ref name="Eisen" /> Furthermore, he suggested that this "phylogenomic" approach could be used as a general method for prediction functions of genes. This approach was formally described in 1998.<ref>{{cite journal | vauthors = Eisen JA | title = Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis | journal = Genome Research | volume = 8 | issue = 3 | pages = 163–167 | date = March 1998 | pmid = 9521918 | doi = 10.1101/gr.8.3.163 | doi-access = free }}</ref> For reviews of this aspect of phylogenomics see Brown D, Sjölander K. Functional classification using phylogenomic inference.<ref>{{cite journal | vauthors = Brown D, Sjölander K | title = Functional classification using phylogenomic inference | journal = PLOS Computational Biology | volume = 2 | issue = 6 | pages = e77 | date = June 2006 | pmid = 16846248 | pmc = 1484587 | doi = 10.1371/journal.pcbi.0020077 | bibcode = 2006PLSCB...2...77B | doi-access = free }}</ref><ref>{{cite journal | vauthors = Sjölander K | title = Phylogenomic inference of protein molecular function: advances and challenges | journal = Bioinformatics | volume = 20 | issue = 2 | pages = 170–179 | date = January 2004 | pmid = 14734307 | doi = 10.1093/bioinformatics/bth021 | doi-access = free }}</ref> ==Prediction and retracing lateral gene transfer== Traditional phylogenetic techniques have difficulty establishing differences between genes that are similar because of lateral gene transfer and those that are similar because the organisms shared an ancestor. By comparing large numbers of genes or entire genomes among many species, it is possible to identify transferred genes, since these sequences behave differently from what is expected given the [[taxonomy (biology)|taxonomy]] of the organism. Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer.<ref>{{cite journal | vauthors = Whitaker JW, McConkey GA, Westhead DR | title = The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes | journal = Genome Biology | volume = 10 | issue = 4 | pages = R36 | year = 2009 | pmid = 19368726 | pmc = 2688927 | doi = 10.1186/gb-2009-10-4-r36 | doi-access = free }}</ref> ==Gene family evolution== The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as [[gene duplication]] or [[gene deletion]]. Often, such events are evolutionarily relevant. For example, multiple duplications of genes encoding degradative enzymes of certain families is a common adaptation in microbes to new nutrient sources. On the contrary, loss of genes is important in [[reductive evolution]], such as in intracellular parasites or symbionts. [[Whole genome duplication]] events, which potentially duplicate all the genes in a genome at once, are drastic evolutionary events with great relevance in the evolution of many clades, and whose signal can be traced with phylogenomic methods. ==Establishment of evolutionary relationships== Traditional single-gene studies are effective in establishing phylogenetic trees among closely related organisms, but have drawbacks when comparing more distantly related organisms or microorganisms. This is because of [[lateral gene transfer]], [[Convergent evolution|convergence]], and varying rates of evolution for different genes. By using entire genomes in these comparisons, the anomalies created from these factors are overwhelmed by the pattern of evolution indicated by the majority of the data.<ref>{{cite journal | vauthors = Delsuc F, Brinkmann H, Philippe H | title = Phylogenomics and the reconstruction of the tree of life | journal = Nature Reviews. Genetics | volume = 6 | issue = 5 | pages = 361–375 | date = May 2005 | pmid = 15861208 | doi = 10.1038/nrg1603 | s2cid = 16379422 | citeseerx = 10.1.1.333.1615 }}</ref><ref>Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D "Phylogenomics of eukaryotes: impact of missing data on large alignments ''Mol Biol Evol'' 2004 Sep;21(9):1740-52. .</ref><ref>{{cite journal | vauthors = Jeffroy O, Brinkmann H, Delsuc F, Philippe H | title = Phylogenomics: the beginning of incongruence? | journal = Trends in Genetics | volume = 22 | issue = 4 | pages = 225–231 | date = April 2006 | pmid = 16490279 | doi = 10.1016/j.tig.2006.02.003 | url = https://hal.archives-ouvertes.fr/halsde-00315496/file/Jeffroy-TrendsGenet06_HAL.pdf }}</ref> Through '''phylogenomics''', it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor. Researchers compared 135 genes from 65 different [[species]] of photosynthetic organisms. These included [[plants]], [[alveolates]], [[rhizaria]]ns, [[haptophytes]] and [[cryptomonads]].<ref>{{cite journal | vauthors = Burki F, Shalchian-Tabrizi K, Pawlowski J | title = Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes | journal = Biology Letters | volume = 4 | issue = 4 | pages = 366–369 | date = August 2008 | pmid = 18522922 | pmc = 2610160 | doi = 10.1098/rsbl.2008.0224 }}</ref> This has been referred to as the [[Plants+HC+SAR megagroup]]. Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately.<ref name="Dos Reis2012">{{cite journal | vauthors = dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, Yang Z | title = Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny | journal = Proceedings. Biological Sciences | volume = 279 | issue = 1742 | pages = 3491–3500 | date = September 2012 | pmid = 22628470 | pmc = 3396900 | doi = 10.1098/rspb.2012.0683 }}</ref><ref>{{cite journal | vauthors = Kober KM, Bernardi G | title = Phylogenomics of strongylocentrotid sea urchins | journal = BMC Evolutionary Biology | volume = 13 | pages = 88 | date = April 2013 | pmid = 23617542 | pmc = 3637829 | doi = 10.1186/1471-2148-13-88 | doi-access = free }}</ref> However, in practice this is not always the case. Due to insufficient data, multiple trees can sometimes be supported by the same data when analyzed using different methods.<ref>{{cite journal|last=Philippe|first=Herve'|author2=Delsuc, Frederic |author3=Brinkmann, Henner |author4= Lartillot, Nicolas |title=Phylogenomics|journal=Annual Review of Ecology, Evolution, and Systematics|year=2005|volume=36|pages=541–562|doi=10.1146/annurev.ecolsys.35.112202.130205}}</ref> ==Databases== # [[PhylomeDB]] == See also == * ''[[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]]'' (phylogenomics software) * [[Microbial phylogenetics]] * [[Phylogenetics]] * [[Sequence alignment]] * [[Supertree]] == References == {{reflist|2}} {{Phylogenetics}} [[Category:Genomics]] [[Category:Phylogenetics]] </textarea><div class="templatesUsed"><div class="mw-templatesUsedExplanation"><p><span id="templatesused">Pages transcluded onto the current version of this page<span class="posteditwindowhelplinks"> (<a href="/wiki/Help:Transclusion" title="Help:Transclusion">help</a>)</span>:</span> </p></div><ul> <li><a href="/wiki/Template:Cite_book" title="Template:Cite book">Template:Cite book</a> (<a href="/w/index.php?title=Template:Cite_book&action=edit" title="Template:Cite book">view source</a>) (protected)</li><li><a href="/wiki/Template:Cite_journal" title="Template:Cite journal">Template:Cite journal</a> (<a href="/w/index.php?title=Template:Cite_journal&action=edit" title="Template:Cite journal">view source</a>) (protected)</li><li><a href="/wiki/Template:Hlist/styles.css" title="Template:Hlist/styles.css">Template:Hlist/styles.css</a> (<a href="/w/index.php?title=Template:Hlist/styles.css&action=edit" title="Template:Hlist/styles.css">view source</a>) (protected)</li><li><a href="/wiki/Template:Icon" title="Template:Icon">Template:Icon</a> (<a href="/w/index.php?title=Template:Icon&action=edit" title="Template:Icon">view source</a>) (template editor protected)</li><li><a href="/wiki/Template:Main_other" title="Template:Main other">Template:Main other</a> (<a href="/w/index.php?title=Template:Main_other&action=edit" title="Template:Main other">view source</a>) (protected)</li><li><a href="/wiki/Template:Navbox" title="Template:Navbox">Template:Navbox</a> (<a href="/w/index.php?title=Template:Navbox&action=edit" title="Template:Navbox">view source</a>) (template editor protected)</li><li><a href="/wiki/Template:Pagetype" title="Template:Pagetype">Template:Pagetype</a> (<a href="/w/index.php?title=Template:Pagetype&action=edit" title="Template:Pagetype">view source</a>) (protected)</li><li><a href="/wiki/Template:Phylogenetics" title="Template:Phylogenetics">Template:Phylogenetics</a> (<a href="/w/index.php?title=Template:Phylogenetics&action=edit" title="Template:Phylogenetics">edit</a>) </li><li><a href="/wiki/Template:Portal" title="Template:Portal">Template:Portal</a> (<a href="/w/index.php?title=Template:Portal&action=edit" title="Template:Portal">view source</a>) (template editor protected)</li><li><a href="/wiki/Template:Reflist" title="Template:Reflist">Template:Reflist</a> (<a href="/w/index.php?title=Template:Reflist&action=edit" title="Template:Reflist">view source</a>) (protected)</li><li><a href="/wiki/Template:Reflist/styles.css" title="Template:Reflist/styles.css">Template:Reflist/styles.css</a> (<a href="/w/index.php?title=Template:Reflist/styles.css&action=edit" title="Template:Reflist/styles.css">view source</a>) (protected)</li><li><a href="/wiki/Template:SDcat" title="Template:SDcat">Template:SDcat</a> (<a href="/w/index.php?title=Template:SDcat&action=edit" title="Template:SDcat">view source</a>) (protected)</li><li><a href="/wiki/Template:Short_description" title="Template:Short description">Template:Short description</a> (<a href="/w/index.php?title=Template:Short_description&action=edit" title="Template:Short description">view source</a>) (protected)</li><li><a href="/wiki/Template:Short_description/lowercasecheck" title="Template:Short description/lowercasecheck">Template:Short description/lowercasecheck</a> (<a href="/w/index.php?title=Template:Short_description/lowercasecheck&action=edit" title="Template:Short description/lowercasecheck">view source</a>) (protected)</li><li><a href="/wiki/Module:Arguments" title="Module:Arguments">Module:Arguments</a> (<a href="/w/index.php?title=Module:Arguments&action=edit" title="Module:Arguments">view source</a>) (protected)</li><li><a href="/wiki/Module:Check_for_unknown_parameters" title="Module:Check for unknown parameters">Module:Check for unknown parameters</a> (<a href="/w/index.php?title=Module:Check_for_unknown_parameters&action=edit" title="Module:Check for unknown parameters">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1" title="Module:Citation/CS1">Module:Citation/CS1</a> (<a href="/w/index.php?title=Module:Citation/CS1&action=edit" title="Module:Citation/CS1">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/COinS" title="Module:Citation/CS1/COinS">Module:Citation/CS1/COinS</a> (<a href="/w/index.php?title=Module:Citation/CS1/COinS&action=edit" title="Module:Citation/CS1/COinS">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/Configuration" title="Module:Citation/CS1/Configuration">Module:Citation/CS1/Configuration</a> (<a href="/w/index.php?title=Module:Citation/CS1/Configuration&action=edit" title="Module:Citation/CS1/Configuration">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/Date_validation" title="Module:Citation/CS1/Date validation">Module:Citation/CS1/Date validation</a> (<a href="/w/index.php?title=Module:Citation/CS1/Date_validation&action=edit" title="Module:Citation/CS1/Date validation">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/Identifiers" title="Module:Citation/CS1/Identifiers">Module:Citation/CS1/Identifiers</a> (<a href="/w/index.php?title=Module:Citation/CS1/Identifiers&action=edit" title="Module:Citation/CS1/Identifiers">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/Utilities" title="Module:Citation/CS1/Utilities">Module:Citation/CS1/Utilities</a> (<a href="/w/index.php?title=Module:Citation/CS1/Utilities&action=edit" title="Module:Citation/CS1/Utilities">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/Whitelist" title="Module:Citation/CS1/Whitelist">Module:Citation/CS1/Whitelist</a> (<a href="/w/index.php?title=Module:Citation/CS1/Whitelist&action=edit" title="Module:Citation/CS1/Whitelist">view source</a>) (protected)</li><li><a href="/wiki/Module:Citation/CS1/styles.css" title="Module:Citation/CS1/styles.css">Module:Citation/CS1/styles.css</a> (<a href="/w/index.php?title=Module:Citation/CS1/styles.css&action=edit" title="Module:Citation/CS1/styles.css">view source</a>) (protected)</li><li><a href="/wiki/Module:Disambiguation/templates" title="Module:Disambiguation/templates">Module:Disambiguation/templates</a> (<a href="/w/index.php?title=Module:Disambiguation/templates&action=edit" title="Module:Disambiguation/templates">view source</a>) (protected)</li><li><a href="/wiki/Module:Icon" title="Module:Icon">Module:Icon</a> (<a href="/w/index.php?title=Module:Icon&action=edit" title="Module:Icon">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Icon/data" title="Module:Icon/data">Module:Icon/data</a> (<a href="/w/index.php?title=Module:Icon/data&action=edit" title="Module:Icon/data">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Navbar" title="Module:Navbar">Module:Navbar</a> (<a href="/w/index.php?title=Module:Navbar&action=edit" title="Module:Navbar">view source</a>) (protected)</li><li><a href="/wiki/Module:Navbar/configuration" title="Module:Navbar/configuration">Module:Navbar/configuration</a> (<a href="/w/index.php?title=Module:Navbar/configuration&action=edit" title="Module:Navbar/configuration">view source</a>) (protected)</li><li><a href="/wiki/Module:Navbar/styles.css" title="Module:Navbar/styles.css">Module:Navbar/styles.css</a> (<a href="/w/index.php?title=Module:Navbar/styles.css&action=edit" title="Module:Navbar/styles.css">view source</a>) (protected)</li><li><a href="/wiki/Module:Navbox" title="Module:Navbox">Module:Navbox</a> (<a href="/w/index.php?title=Module:Navbox&action=edit" title="Module:Navbox">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Navbox/configuration" title="Module:Navbox/configuration">Module:Navbox/configuration</a> (<a href="/w/index.php?title=Module:Navbox/configuration&action=edit" title="Module:Navbox/configuration">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Navbox/styles.css" title="Module:Navbox/styles.css">Module:Navbox/styles.css</a> (<a href="/w/index.php?title=Module:Navbox/styles.css&action=edit" title="Module:Navbox/styles.css">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Pagetype" title="Module:Pagetype">Module:Pagetype</a> (<a href="/w/index.php?title=Module:Pagetype&action=edit" title="Module:Pagetype">view source</a>) (protected)</li><li><a href="/wiki/Module:Pagetype/config" title="Module:Pagetype/config">Module:Pagetype/config</a> (<a href="/w/index.php?title=Module:Pagetype/config&action=edit" title="Module:Pagetype/config">view source</a>) (protected)</li><li><a href="/wiki/Module:Pagetype/disambiguation" class="mw-redirect" title="Module:Pagetype/disambiguation">Module:Pagetype/disambiguation</a> (<a href="/w/index.php?title=Module:Pagetype/disambiguation&action=edit" class="mw-redirect" title="Module:Pagetype/disambiguation">view source</a>) (protected)</li><li><a href="/wiki/Module:Pagetype/rfd" title="Module:Pagetype/rfd">Module:Pagetype/rfd</a> (<a href="/w/index.php?title=Module:Pagetype/rfd&action=edit" title="Module:Pagetype/rfd">view source</a>) (protected)</li><li><a href="/wiki/Module:Pagetype/setindex" title="Module:Pagetype/setindex">Module:Pagetype/setindex</a> (<a href="/w/index.php?title=Module:Pagetype/setindex&action=edit" title="Module:Pagetype/setindex">view source</a>) (protected)</li><li><a href="/wiki/Module:Pagetype/softredirect" title="Module:Pagetype/softredirect">Module:Pagetype/softredirect</a> (<a href="/w/index.php?title=Module:Pagetype/softredirect&action=edit" title="Module:Pagetype/softredirect">view source</a>) (protected)</li><li><a href="/wiki/Module:Portal" title="Module:Portal">Module:Portal</a> (<a href="/w/index.php?title=Module:Portal&action=edit" title="Module:Portal">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Portal/images/e" title="Module:Portal/images/e">Module:Portal/images/e</a> (<a href="/w/index.php?title=Module:Portal/images/e&action=edit" title="Module:Portal/images/e">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:Portal/styles.css" title="Module:Portal/styles.css">Module:Portal/styles.css</a> (<a href="/w/index.php?title=Module:Portal/styles.css&action=edit" title="Module:Portal/styles.css">view source</a>) (template editor protected)</li><li><a href="/wiki/Module:SDcat" title="Module:SDcat">Module:SDcat</a> (<a href="/w/index.php?title=Module:SDcat&action=edit" title="Module:SDcat">view source</a>) (protected)</li><li><a href="/wiki/Module:String" title="Module:String">Module:String</a> (<a href="/w/index.php?title=Module:String&action=edit" title="Module:String">view source</a>) (protected)</li><li><a href="/wiki/Module:TableTools" title="Module:TableTools">Module:TableTools</a> (<a href="/w/index.php?title=Module:TableTools&action=edit" title="Module:TableTools">view source</a>) (protected)</li><li><a href="/wiki/Module:Wikitext_Parsing" title="Module:Wikitext Parsing">Module:Wikitext Parsing</a> (<a href="/w/index.php?title=Module:Wikitext_Parsing&action=edit" title="Module:Wikitext Parsing">view source</a>) (protected)</li><li><a href="/wiki/Module:Yesno" title="Module:Yesno">Module:Yesno</a> (<a href="/w/index.php?title=Module:Yesno&action=edit" title="Module:Yesno">view source</a>) (protected)</li></ul></div><p id="mw-returnto">Return to <a href="/wiki/Phylogenomics" title="Phylogenomics">Phylogenomics</a>.</p> <noscript><img src="https://login.wikimedia.org/wiki/Special:CentralAutoLogin/start?type=1x1" alt="" width="1" height="1" style="border: none; position: absolute;"></noscript> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" href="https://en.wikipedia.org/wiki/Phylogenomics">https://en.wikipedia.org/wiki/Phylogenomics</a>"</div></div> <div id="catlinks" class="catlinks catlinks-allhidden" data-mw="interface"></div> </div> </main> </div> <div class="mw-footer-container"> <footer id="footer" class="mw-footer" > <ul id="footer-info"> </ul> <ul id="footer-places"> <li id="footer-places-privacy"><a href="https://foundation.wikimedia.org/wiki/Special:MyLanguage/Policy:Privacy_policy">Privacy policy</a></li> <li id="footer-places-about"><a href="/wiki/Wikipedia:About">About Wikipedia</a></li> <li id="footer-places-disclaimers"><a href="/wiki/Wikipedia:General_disclaimer">Disclaimers</a></li> <li id="footer-places-contact"><a href="//en.wikipedia.org/wiki/Wikipedia:Contact_us">Contact Wikipedia</a></li> <li id="footer-places-wm-codeofconduct"><a href="https://foundation.wikimedia.org/wiki/Special:MyLanguage/Policy:Universal_Code_of_Conduct">Code of Conduct</a></li> <li id="footer-places-developers"><a href="https://developer.wikimedia.org">Developers</a></li> <li id="footer-places-statslink"><a href="https://stats.wikimedia.org/#/en.wikipedia.org">Statistics</a></li> <li id="footer-places-cookiestatement"><a href="https://foundation.wikimedia.org/wiki/Special:MyLanguage/Policy:Cookie_statement">Cookie statement</a></li> <li id="footer-places-mobileview"><a href="//en.m.wikipedia.org/w/index.php?title=Phylogenomics&action=edit&mobileaction=toggle_view_mobile" class="noprint stopMobileRedirectToggle">Mobile view</a></li> </ul> <ul id="footer-icons" class="noprint"> <li id="footer-copyrightico"><a href="https://wikimediafoundation.org/" class="cdx-button cdx-button--fake-button cdx-button--size-large cdx-button--fake-button--enabled"><img src="/static/images/footer/wikimedia-button.svg" width="84" height="29" alt="Wikimedia Foundation" loading="lazy"></a></li> <li id="footer-poweredbyico"><a href="https://www.mediawiki.org/" class="cdx-button cdx-button--fake-button cdx-button--size-large cdx-button--fake-button--enabled"><img src="/w/resources/assets/poweredby_mediawiki.svg" alt="Powered by MediaWiki" width="88" height="31" loading="lazy"></a></li> </ul> </footer> </div> </div> </div> <div class="vector-settings" id="p-dock-bottom"> <ul></ul> </div><script>(RLQ=window.RLQ||[]).push(function(){mw.config.set({"wgHostname":"mw-web.codfw.main-f69cdc8f6-4dnzt","wgBackendResponseTime":332,"wgPageParseReport":{"limitreport":{"cputime":"0.066","walltime":"0.087","ppvisitednodes":{"value":418,"limit":1000000},"postexpandincludesize":{"value":17740,"limit":2097152},"templateargumentsize":{"value":6556,"limit":2097152},"expansiondepth":{"value":9,"limit":100},"expensivefunctioncount":{"value":0,"limit":500},"unstrip-depth":{"value":0,"limit":20},"unstrip-size":{"value":469,"limit":5000000},"entityaccesscount":{"value":0,"limit":400},"timingprofile":["100.00% 60.813 1 -total"," 99.86% 60.728 2 Template:Blocked_text"," 42.68% 25.954 2 Template:Replace"," 38.44% 23.378 1 Template:Colocationwebhost"," 35.00% 21.282 1 Template:Hidden"," 16.06% 9.769 1 Template:Hidden_begin"," 13.70% 8.333 1 Template:Tlx"," 2.16% 1.315 1 MediaWiki:Wikimedia-globalblocking-blockedtext-mistake"," 1.83% 1.111 1 Template:Hidden_end"," 1.77% 1.078 1 MediaWiki:Wikimedia-globalblocking-blockedtext-mistake-email-steward"]},"scribunto":{"limitreport-timeusage":{"value":"0.013","limit":"10.000"},"limitreport-memusage":{"value":1043257,"limit":52428800}},"cachereport":{"origin":"mw-web.codfw.main-f69cdc8f6-4dnzt","timestamp":"20241124115614","ttl":2592000,"transientcontent":false}}});});</script> </body> </html>