{"id":186,"date":"2018-08-24T13:30:51","date_gmt":"2018-08-24T11:30:51","guid":{"rendered":"https:\/\/project.inria.fr\/treerecs\/?page_id=186"},"modified":"2020-06-11T12:21:54","modified_gmt":"2020-06-11T10:21:54","slug":"get-treerecs","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/treerecs\/get-treerecs\/","title":{"rendered":"Get Treerecs"},"content":{"rendered":"<h2 id=\"binaries\">1) Binaries<\/h2>\n<p>The simplest way to get Treerecs is to download the precompiled binaries.<\/p>\n<ul>\n<li>GNU\/Linux &amp; OS X<\/li>\n<p><a href=\"https:\/\/bioconda.github.io\/recipes\/treerecs\/README.html\">install treerecs with bioconda<\/a><\/p>\n<li>Windows<\/li>\n<p>We advise windows users to run Treerecs via <a href=\"https:\/\/doua.prabi.fr\/software\/seaview\">Seaview<\/a>.<br \/>\n    Install 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.<\/p>\n<p>If you want to use Treerecs without Seaview, you can download binaries from the <a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/-\/tags\">gitlab page<\/a> or find the latest version (1.2) here: <a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/uploads\/54734eda6a3d8433d0e2a5c2731744d8\/treerecs.exe\">treerecs.exe<\/a><\/p>\n<\/ul>\n<h2 id=\"source\">2) Build from source<\/h2>\n<p>Alternatively, you can download the source code and compile it yourself.<br \/>\nThis should be straightforward since the only requirements are <a href=\"https:\/\/cmake.org\/\">CMake<\/a> and a C++14-capable compiler.<\/p>\n<h3 id=\"source\">2.1) Get the source code<\/h3>\n<h4 id=\"source\">2.1.1) Download<\/h4>\n<p><a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/-\/archive\/v1.2\/Treerecs-v1.2.zip\">Latest release (zip)<\/a><br \/>\n<a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/-\/archive\/v1.2\/Treerecs-v1.2.tar.gz\">Latest release (tar gz)<\/a><br \/>\n<br \/>\n<a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/repository\/archive.zip?ref=dev\">Development version (unstable) (zip)<\/a><br \/>\n<a href=\"https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\/repository\/archive.tar.gz?ref=dev\">Development version (unstable) (tar gz)<\/a><\/p>\n<h4 id=\"source\">2.1.2) Clone the git repository<\/h4>\n<p>If you wish to stay tuned and always have the latest version of Treerecs at hand, you can clone the git repository:<\/p>\n<ul>\n<li>using https:<br \/>\n    <code>git clone https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs.git<\/code>\n  <\/li>\n<li>or using ssh (requires a registered ssh key):<br \/>\n    <code>git clone git@gitlab.inria.fr:Phylophile\/Treerecs.git<\/code>\n  <\/li>\n<\/ul>\n<p>See also the <a href=\" https:\/\/gitlab.inria.fr\/Phylophile\/Treerecs\">gitlab page<\/a>.<\/p>\n<h3 id=\"source\">2.2) Build Treerecs<\/h3>\n<p>Open a terminal and cd into the Treerecs directory<\/p>\n<p>From the Treerecs directory run the following commands:<br \/>\n<code><br \/>\n  cmake -DCMAKE_BUILD_TYPE=Release .<br \/>\n  make<br \/>\n<\/code><\/p>\n<p>The created executable can be found in the <em>bin<\/em> directory.<br \/>\nYou can try <i>e.g.<\/i>:<br \/>\n<code><br \/>\n    .\/bin\/treerecs --help<br \/>\n<\/code><\/p>\n<h3 id=\"source\">2.3) Install Treerecs (optional)<\/h3>\n<p>If you wish to install Treerecs on your system, run the following command from the Treerecs directory:<br \/>\n<code><br \/>\n  sudo make install<br \/>\n<\/code><\/p>\n<p>To uninstall Treerecs:<br \/>\n<code><br \/>\n  sudo make uninstall<br \/>\n<\/code><\/p>\n","protected":false},"excerpt":{"rendered":"<p>1) Binaries The simplest way to get Treerecs is to download the precompiled binaries. GNU\/Linux &amp; OS X install treerecs with bioconda Windows We advise windows users to run Treerecs via Seaview. Install and launch Seaview, then open a gene tree file (for instance one of those provided in the\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/treerecs\/get-treerecs\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":972,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-186","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/186","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\/972"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/comments?post=186"}],"version-history":[{"count":17,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/186\/revisions"}],"predecessor-version":[{"id":384,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/186\/revisions\/384"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/media?parent=186"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}