{"id":187655,"date":"2015-08-21T01:42:22","date_gmt":"2015-08-21T09:42:22","guid":{"rendered":"http:\/\/www.unz.com\/?post_type=gnxp&p=64516"},"modified":"-0001-11-30T00:00:00","modified_gmt":"-0001-11-30T08:00:00","slug":"clumpak-for-model-based-population-structure-analysis","status":"publish","type":"post","link":"https:\/\/www.gnxp.com\/WordPress\/2015\/08\/21\/clumpak-for-model-based-population-structure-analysis\/","title":{"rendered":"CLUMPAK, for model-based population structure analysis"},"content":{"rendered":"

This isn’t probably aimed at most readers, but I think it’s important to pass the word around, so, Clumpak: a program for identifying clustering modes and packaging population structure inferences across K<\/a>. An ungated version<\/a>. From the abstract:<\/p>\n

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted\u00a0<\/span>K<\/em>), examines multiple independent runs for each fixed value of\u00a0<\/span>K<\/em>, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present\u00a0<\/span>clumpak<\/span>\u00a0(Cluster Markov Packager Across\u00a0<\/span>K<\/em>), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single\u00a0<\/span>K<\/em>\u00a0value,\u00a0<\/span>clumpak<\/span>\u00a0identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software\u00a0<\/span>clumpp<\/span>. Next,\u00a0<\/span>clumpak<\/span>\u00a0identifies an optimal alignment of inferred clusters across different values of\u00a0<\/span>K<\/em>, extending a similar approach implemented for a fixed\u00a0<\/span>K<\/em>\u00a0in\u00a0<\/span>clumpp<\/span>\u00a0and simplifying the comparison of clustering results across different\u00a0<\/span>K<\/em>\u00a0values.\u00a0<\/span>clumpak<\/span>\u00a0incorporates additional features, such as implementations of methods for choosing\u00a0<\/span>K<\/em>\u00a0and comparing solutions obtained by different programs, models, or data subsets.\u00a0<\/span>clumpak<\/span>, available at\u00a0<\/span>http:\/\/clumpak.tau.ac.il<\/a>, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.<\/span><\/p><\/blockquote>\n

The website deploys the package as a web based application<\/a> (kind of like Structure-harvester). I don’t do GUIs, but I thought I would mention it (the package is downloadable). I’ve shied away from posting admixture barplots not because I think they lack utility. Rather, over the years readers have had a hard time understanding their limitations, and tend to reify a little too much for my taste.<\/b><\/p>\n","protected":false},"excerpt":{"rendered":"

This isn’t probably aimed at most readers, but I think it’s important to pass the word around, so, Clumpak: a program for identifying clustering modes and packaging population structure inferences […]<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_exactmetrics_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0,"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[],"tags":[],"class_list":["post-187655","post","type-post","status-publish","format-standard","hentry"],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/pawqfx-MOH","jetpack-related-posts":[],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/posts\/187655","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/comments?post=187655"}],"version-history":[{"count":0,"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/posts\/187655\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/media?parent=187655"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/categories?post=187655"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.gnxp.com\/WordPress\/wp-json\/wp\/v2\/tags?post=187655"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}