{"id":342,"date":"2019-01-17T08:02:33","date_gmt":"2019-01-17T07:02:33","guid":{"rendered":"http:\/\/wp.unil.ch\/phylo\/?page_id=342"},"modified":"2021-09-30T14:33:07","modified_gmt":"2021-09-30T12:33:07","slug":"fastcodeml","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/phylo\/tools\/fastcodeml\/","title":{"rendered":"FastCodeML"},"content":{"rendered":"<div data-bolt-field=\"teaser\">\n<p>FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol). Although the model is similar to the one implemented in the codeml software from the\u00a0<a href=\"https:\/\/abacus.gene.ucl.ac.uk\/software\/paml.html\">PAML<\/a>\u00a0package, our goal was to focus on the computational efficiency by developing an improved serial implementation but also provide new parallelisation strategies.<\/p>\n<p>By using an hybrid (OpenMP\/MPI) strategy, FastCodeML can reach a speed-up of up to 10 times compared with codeml. The speed-up will increase with larger data sets.<\/p>\n<\/div>\n<div data-bolt-field=\"body\">\n<p>To download, please use the\u00a0<a href=\"https:\/\/selectome.org\/ftp\/FastCodeML\/\">ftp server<\/a>\u00a0of the Swiss Institute of Bioinformatics.<\/p>\n<p align=\"justify\">For questions, please send an email to selectome [at]\u00a0unil.ch<\/p>\n<h3>Reference<\/h3>\n<p>When using this software, please cite:<\/p>\n<address>Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Optimisation strategies for fast detection of positive selection on phylogenetic trees.\u00a0<i>Bioinformatics 30(8): 1129.1137.<\/i><\/address>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol). Although the model is similar to the one implemented in the codeml<\/p>\n","protected":false},"author":1124,"featured_media":0,"parent":132,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-342","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/342","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/users\/1124"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/comments?post=342"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/342\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/132"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/media?parent=342"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}