{"id":1081,"date":"2011-07-19T12:10:14","date_gmt":"2011-07-19T10:10:14","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2011\/07\/19\/evolution-of-the-cape-sedges"},"modified":"2022-09-26T20:01:31","modified_gmt":"2022-09-26T18:01:31","slug":"evolution-of-the-cape-sedges","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/","title":{"rendered":"Evolution of the Cape Sedges"},"content":{"rendered":"Jack Viljoen, a masters student in the Botany department is working on the evolution of Cape Sedges.\r\nFor reconstructing the evolutionary trees of groups like the Cypereae and Schoeneae (Fig. 1),\r\n\r\n<img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/Fig1.png\" alt=\"Mr Bayes\" width=\"371\" height=\"329\" border=\"0\" \/>\r\n\r\n.... we use Monte Carlo Markov Chain (MCMC) sampling to estimate parameter values related to models of DNA sequence evolution.\u00a0 This involves running programs like MrBayes for about 5\u201350 million iterations, in order to explore parameter space to find the region of highest likelihood (Fig. 2a), and to sample this region sufficiently to get good parameter estimates (Fig. 2b).\r\n\r\n<img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/Fig2.png\" alt=\"Mr Bayes\" width=\"408\" height=\"280\" border=\"0\" \/>\r\n\r\nThis process is made much more efficient by running multiple instances of the sampler simultaneously on different CPUs, and we are grateful to the HPC unit at UCT for allowing us to do just that.","protected":false},"excerpt":{"rendered":"<p>    Jack Viljoen, a masters student in the Botany department is working on the evolution of Cape Sedges. For reconstructing the evolutionary trees of groups like the Cypereae and Schoeneae (Fig. 1),&#8230;. we use Monte Carlo Markov Chain (MCMC) sampling &#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9,4],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Evolution of the Cape Sedges - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Evolution of the Cape Sedges - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"Jack Viljoen, a masters student in the Botany department is working on the evolution of Cape Sedges. For reconstructing the evolutionary trees of groups like the Cypereae and Schoeneae (Fig. 1),.... we use Monte Carlo Markov Chain (MCMC) sampling ...\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2011-07-19T10:10:14+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-26T18:01:31+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/Fig1.png\" \/>\n<meta name=\"author\" content=\"Timothy Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Timothy Carr\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\"},\"author\":{\"name\":\"Timothy Carr\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/41f6cd039836d7741f2b82a7b7cfe8d0\"},\"headline\":\"Evolution of the Cape Sedges\",\"datePublished\":\"2011-07-19T10:10:14+00:00\",\"dateModified\":\"2022-09-26T18:01:31+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\"},\"wordCount\":127,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"application\",\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/19\/evolution-of-the-cape-sedges\/\",\"name\":\"Evolution of the Cape Sedges - 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