{"id":2158,"date":"2024-10-24T14:04:00","date_gmt":"2024-10-24T12:04:00","guid":{"rendered":"https:\/\/jakobssonlab.iob.uu.se\/?page_id=2158"},"modified":"2025-02-10T13:24:26","modified_gmt":"2025-02-10T12:24:26","slug":"clumpp","status":"publish","type":"page","link":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/software\/clumpp\/","title":{"rendered":"CLUMPP"},"content":{"rendered":"\n<div class=\"wp-block-group is-layout-constrained wp-block-group-is-layout-constrained\">\n<h1 class=\"wp-block-heading is-style-underlined-heading\">CLUMPP<\/h1>\n\n\n\n<h3 class=\"wp-block-heading\">CLUster Matching and Permutation Program<\/h3>\n\n\n\n<p>CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as <a href=\"http:\/\/pritchardlab.stanford.edu\/structure.html\" target=\"_blank\" rel=\"noopener\">structure<\/a>, <a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/tess.html\" target=\"_blank\" rel=\"noopener\">TESS<\/a>, or <a href=\"http:\/\/www.helsinki.fi\/bsg\/software\/\" target=\"_blank\" rel=\"noopener\">BAPS<\/a>, so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment. A program note describing CLUMPP was published in <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/full\/23\/14\/1801\" target=\"_blank\" rel=\"noopener\">Jakobsson &amp; Rosenberg (2007)<\/a>.&nbsp;CLUMPP was written by Mattias Jakobsson.<\/p>\n\n\n\n<figure class=\"wp-block-image alignleft size-full\"><img decoding=\"async\" src=\"https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2024\/05\/Topology3.jpg\" alt=\"\" class=\"wp-image-1367\" style=\"aspect-ratio:4\/3;object-fit:contain\"\/><\/figure>\n\n\n\n<p>To be redirected to the CLUMPP page at the Rosenbergs Lab, Stanford University,&nbsp;<a href=\"https:\/\/web.stanford.edu\/group\/rosenberglab\/clumpp.html\" target=\"_blank\" rel=\"noopener\">click here<\/a>.<\/p>\n\n\n\n<p>Comments or problems with&nbsp;CLUMPP&nbsp;should be sent to&nbsp;Mattias Jakobsson.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>CLUMPP CLUster Matching and Permutation Program CLUMPP is a program that deals with label switching and multimodality problems in population-genetic [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":2155,"parent":16,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-no-title","meta":{"footnotes":""},"class_list":["post-2158","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2158","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/comments?post=2158"}],"version-history":[{"count":2,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2158\/revisions"}],"predecessor-version":[{"id":2688,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2158\/revisions\/2688"}],"up":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/16"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/media\/2155"}],"wp:attachment":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/media?parent=2158"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}