{"id":3064,"date":"2025-10-21T14:53:50","date_gmt":"2025-10-21T12:53:50","guid":{"rendered":"https:\/\/jakobssonlab.iob.uu.se\/?page_id=3064"},"modified":"2025-10-21T15:50:20","modified_gmt":"2025-10-21T13:50:20","slug":"tt-tto","status":"publish","type":"page","link":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/software\/tt-tto\/","title":{"rendered":"TT.TTo"},"content":{"rendered":"\n<h1 class=\"wp-block-heading is-style-underlined-heading\">TT.TTo<\/h1>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-28f84493 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"732\" height=\"976\" src=\"https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2025\/10\/Software-TT.To-Splitmodel.jpg\" alt=\"TT.TTo Split model \" class=\"wp-image-3065\" srcset=\"https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2025\/10\/Software-TT.To-Splitmodel.jpg 732w, https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2025\/10\/Software-TT.To-Splitmodel-225x300.jpg 225w, https:\/\/jakobssonlab.iob.uu.se\/wp-content\/uploads\/2025\/10\/Software-TT.To-Splitmodel-574x765.jpg 574w\" sizes=\"auto, (max-width: 732px) 100vw, 732px\" \/><figcaption class=\"wp-element-caption\">Simple split model<\/figcaption><\/figure>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<p>By counting the number of derived variants in&nbsp;two samples of size two (one sample of size two&nbsp;from each of the&nbsp;two sub-populations) in a simple split model (see figure), TT estimates all parameters. Specifically,&nbsp;each&nbsp;split time (in generations scaled by the mutation rate) is estimated&nbsp;separately. TT assumes a model with a constant ancestral&nbsp;population size (NA&nbsp;in the figure). TTo alleviates this assumption but requires an appropriate&nbsp;outgroup.&nbsp;<\/p>\n<\/div>\n<\/div>\n\n\n\n<p>The software was created by Per Sj\u00f6din, James McKenna and Mattias Jakobsson.<\/p>\n\n\n\n<h6 class=\"wp-block-heading\">Reference:<\/h6>\n\n\n\n<p>Sj\u00f6din, P., McKenna, J. &amp; Jakobsson, M. (2021). Estimating divergence times from DNA sequences,&nbsp;<em>Genetics<\/em>, Volume 217, Issue 4, iyab008,&nbsp;<a href=\"https:\/\/doi.org\/10.1093\/genetics\/iyab008\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1093\/genetics\/iyab008<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>TT.TTo By counting the number of derived variants in&nbsp;two samples of size two (one sample of size two&nbsp;from each of [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":16,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-no-title","meta":{"footnotes":""},"class_list":["post-3064","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/3064","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=3064"}],"version-history":[{"count":4,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/3064\/revisions"}],"predecessor-version":[{"id":3074,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/3064\/revisions\/3074"}],"up":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/16"}],"wp:attachment":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/media?parent=3064"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}