{"id":4,"date":"2011-12-08T11:55:34","date_gmt":"2011-12-08T11:55:34","guid":{"rendered":"http:\/\/project.inria.fr\/template1\/?page_id=4"},"modified":"2020-03-31T18:35:16","modified_gmt":"2020-03-31T16:35:16","slug":"home","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/treerecs\/","title":{"rendered":""},"content":{"rendered":"<p><\/p>\n<h2 id=\"treerecs\">What is <em>Treerecs<\/em>?<\/h2>\n<p><em>Treerecs<\/em> is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence.<br \/>\nIt can <strong>correct<\/strong>, <strong>rearrange<\/strong> and (re-)<strong>root<\/strong> gene trees with regard to a given species tree.<br \/>\nIt was designed to be both <strong>efficient<\/strong> and <strong>easy to install and to use<\/strong>.<\/p>\n<p><!-- -------------------- Availability -------------------- --><\/p>\n<h2 id=\"availability\">Availability<\/h2>\n<ul>\n<li>Linux<\/li>\n<li>Mac OS<\/li>\n<li>Windows<\/li>\n<\/ul>\n<p><!-- -------------------- Features -------------------- --><\/p>\n<h2 id=\"features\">Features<\/h2>\n<ul>\n<li><strong>Correct<\/strong> gene trees with regard to a reference species tree<\/li>\n<li><strong>Root<\/strong> or re-root gene trees<\/li>\n<li><strong>Contract<\/strong> gene-tree branches whose support is lower than a given threshold, thus creating polytomies (multifurcations) that can be resolved therefater<\/li>\n<li>Sample solutions with equivalent scores<\/li>\n<li>Produce a graphical representation of the reconciled trees<\/li>\n<\/ul>\n<p><!-- -------------------- Formats -------------------- --><\/p>\n<h2 id=\"formats\">Supported formats<\/h2>\n<p><em>Treerecs<\/em> supports the following formats:<\/p>\n<ul>\n<li>Newick<\/li>\n<li>NHX<\/li>\n<li>PhyloXML<\/li>\n<li>recPhyloXML<\/li>\n<li>SVG (graphical output)<\/li>\n<\/ul>\n<p><!-- -------------------- SVG example -------------------- --><\/p>\n<h2 id=\"svg-example\">SVG output example<\/h2>\n<div style=\"width: 300px\" class=\"wp-caption alignleft\"><a class=\"click-to-enlarge\" href=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/gene_tree_reconciliation.svg_.png\"><img decoding=\"async\" src=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/gene_tree_reconciliation.svg_-290x300.png\" alt=\"\" \/><\/a><p class=\"wp-caption-text\">An example of SVG output<\/p><\/div>\n<div style=\"clear:both;\"><\/div>\n<p><!-- -------------------- Seaview -------------------- --><\/p>\n<h2 id=\"seaview\">Use Treerecs with Seaview <img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/seaview_logo.png\" alt=\"\" width=\"31\" height=\"31\" \/><\/h2>\n<p>Treerecs has been integrated in <a href=\"http:\/\/doua.prabi.fr\/software\/seaview\">Seaview<\/a> with a graphical interface.<br \/>\nInstall and launch Seaview, then open a gene tree file (for instance one of those provided in the examples) and choose &#8220;Reconcile->Reconcile, root and rearrange with Treerecs&#8221; in the menu.<br \/>\n<div id=\"attachment_161\" style=\"width: 572px\" class=\"wp-caption alignleft\"><a class=\"click-to-enlarge\" href=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/treerecs_seaview_preview.png\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-161\" src=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/treerecs_seaview_preview-300x191.png\" alt=\"\" width=\"562\" height=\"358\" \/><\/a><p id=\"caption-attachment-161\" class=\"wp-caption-text\">Preview of Seaview with Treerecs<\/p><\/div><\/p>\n<div style=\"clear:both;\"><\/div>\n<p><!-- -------------------- Contributors -------------------- --><\/p>\n<h2 id=\"contributors\">Contributors<\/h2>\n<p>Treerecs is currently developed in the Inria <a href=\"https:\/\/www.inria.fr\/equipes\/beagle\" target=\"_blank\" rel=\"noopener\">Beagle<\/a> team.<\/p>\n<p>Main contributors:<\/p>\n<ul>\n<li>Nicolas Comte<\/li>\n<li>David Parsons<\/li>\n<li>Eric Tannier<\/li>\n<\/ul>\n<p>Other contributors:<\/p>\n<ul>\n<li>Beno\u00eet Morel<\/li>\n<\/ul>\n<p><!-- -------------------- Logos -------------------- --><br \/>\n<a href=\"http:\/\/www.inria.fr\/\" target=\"_blank\" rel=\"noopener\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium\" src=\"https:\/\/project.inria.fr\/treerecs\/files\/2017\/11\/inr_logo_scientifique_eng_v2-300x105.png\" alt=\"\" width=\"300\" height=\"105\" \/><\/a><a href=\"https:\/\/www.inria.fr\/equipes\/beagle\" target=\"_blank\" rel=\"noopener\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright\" src=\"https:\/\/project.inria.fr\/treerecs\/files\/2011\/12\/beagle_logo_4_bw-300x300.png\" alt=\"\" width=\"223\" height=\"223\" \/><\/a><\/p>","protected":false},"excerpt":{"rendered":"<p>What is Treerecs? Treerecs is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence. It can correct, rearrange and (re-)root gene trees with regard to a given species tree. It was designed to be both efficient and easy to install and to use. Availability Linux\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/treerecs\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":1,"featured_media":72,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-4","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/4","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/comments?post=4"}],"version-history":[{"count":65,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/4\/revisions"}],"predecessor-version":[{"id":379,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/4\/revisions\/379"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/media\/72"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/media?parent=4"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}