{"id":2164,"date":"2024-10-24T14:11:36","date_gmt":"2024-10-24T12:11:36","guid":{"rendered":"https:\/\/jakobssonlab.iob.uu.se\/?page_id=2164"},"modified":"2025-02-10T13:29:15","modified_gmt":"2025-02-10T12:29:15","slug":"pmdtools","status":"publish","type":"page","link":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/software\/pmdtools\/","title":{"rendered":"PMDTools"},"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\">PMDTools<\/h1>\n\n\n\n<h3 class=\"wp-block-heading\">PostMortem Damage Tools<\/h3>\n\n\n\n<p>The program was&nbsp;developed to decipher endogenous, degraded DNA fragments from those derived from&nbsp;modern contaminations in ancient DNA extracts. It implements a likelihood framework utilizing patterns of postmortem damage, base quality scores and biological polymorphisms. The outcome is a sample specific PMD score that indicates, if it is genuinely of ancient material.<\/p>\n\n\n\n<p>The underlying&nbsp;methods were described in <a href=\"http:\/\/www.pnas.org\/content\/111\/6\/2229.abstract\" target=\"_blank\" rel=\"noopener\">Skoglund et al. (2014<\/a>) and the program itself can be downloaded, <a href=\"https:\/\/code.google.com\/p\/pmdtools\/\" target=\"_blank\" rel=\"noopener\">click here<\/a>.<\/p>\n\n\n\n<figure class=\"wp-block-image alignleft size-full is-resized\"><img decoding=\"async\" src=\"https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2024\/05\/Skoglund_2014_PMDtools-3.jpg\" alt=\"\" class=\"wp-image-1348\" style=\"width:779px;height:auto\"\/><\/figure>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>PMDTools PostMortem Damage Tools The program was&nbsp;developed to decipher endogenous, degraded DNA fragments from those derived from&nbsp;modern contaminations in ancient [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":2155,"parent":16,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-no-title","meta":{"footnotes":""},"class_list":["post-2164","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2164","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\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/comments?post=2164"}],"version-history":[{"count":2,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2164\/revisions"}],"predecessor-version":[{"id":2693,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/2164\/revisions\/2693"}],"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=2164"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}