{"id":363,"date":"2025-07-03T23:46:52","date_gmt":"2025-07-03T23:46:52","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=363"},"modified":"2025-07-11T00:03:54","modified_gmt":"2025-07-11T00:03:54","slug":"genetic-similarity-matrix-computation","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/03\/genetic-similarity-matrix-computation\/","title":{"rendered":"Genetic similarity matrix computation"},"content":{"rendered":"\n

Figure 1 shows the tab page selected for calculating the “genetic similarity matrix.”<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

(Figure 1)<\/p>\n\n\n\n

Figure 2 shows the result files listed in the project folder. The file with the CSV extension contains the calculated genetic similarity matrix results.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

(Figure 2)<\/p>\n\n\n\n

Figure 3 shows the resulting genetic similarity matrix. You can see that all diagonal values of the matrix are 1, and all other values are between 0 and 1.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

(Figure 3)<\/p>\n\n\n\n

You can draw dendrograms from the calculated genetic similarity matrix using QTLmax Workbench; by using it, you can draw the following two types of dendrograms:<\/p>\n\n\n\n

    \n
  1. Circular dendrogram<\/li>\n\n\n\n
  2. Plain dendrogram<\/li>\n<\/ol>\n\n\n\n

    Figure 4 shows the tab page in QTLmax Workbench that supports dendrogram plotting. If you find it tedious to manually specify each option, click [Load demo]. You’ll then see all the settings automatically filled in (Figure 4).<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    (Figure 4)<\/p>\n\n\n\n

    After clicking the [Similarity matrix (CSV)] button, you can replace the demo data with your own, followed by changing the settings to your desired values. You can select a number from the combobox on the left side of the [Confirm] button. This number represents how many groups you want to divide the entire population into. Once you select a number, you will see that many buttons below it become active, each labeled (e.g., [Group 1], [Group 2], [Group 3]). Clicking each button will display a pop-up palette where you can choose a color for that specific group. After finalizing all your settings, click the [Visualize] button to draw the dendrogram. Figure 5 shows a dendrogram drawn after dividing the entire population into two groups.<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    (Figure 5)<\/p>\n\n\n\n

    <\/p>\n","protected":false},"excerpt":{"rendered":"

    Figure 1 shows the tab page selected for calculating the “genetic similarity matrix.” (Figure 1) Figure 2 shows the result files listed in the project folder. The file with the CSV extension contains the calculated genetic similarity matrix results. (Figure 2) Figure 3 shows the resulting genetic similarity matrix. You can see that all diagonal […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-363","post","type-post","status-publish","format-standard","hentry","category-guide"],"_links":{"self":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/363","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/comments?post=363"}],"version-history":[{"count":12,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/363\/revisions"}],"predecessor-version":[{"id":604,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/363\/revisions\/604"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=363"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=363"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=363"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}