A program written in C that can perform genomic scans for adaptive introgression using a composite likelihood ratio test.<\/p>\n\n\n\n
Please cite the following manuscript if using this software:<\/strong> On a Linux system, extract the compressed files using the command Note:<\/strong>VolcanoFinder<\/em> should run on a Linux<\/strong> system. We are working to extend this functionality to other Unix-based systems for the future. As an example, on some Mac systems, running VolcanoFinder<\/em> can return an error on some inputs, yet we have not found these errors reproducible on Linux systems. We are working to resolve such issues.<\/p>\n\n\n\n Software history<\/strong> A program written in C that can perform genomic scans for adaptive introgression using a composite likelihood ratio test. Please […]<\/p>\n","protected":false},"author":101,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"normal-width-container","site-content-style":"boxed","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"default","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-160","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/160","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/users\/101"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/comments?post=160"}],"version-history":[{"count":3,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/160\/revisions"}],"predecessor-version":[{"id":163,"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/pages\/160\/revisions\/163"}],"wp:attachment":[{"href":"https:\/\/faculty.eng.fau.edu\/degiorgiogroup\/wp-json\/wp\/v2\/media?parent=160"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
M Setter, S Mousset, X Cheng, R Nielsen, M DeGiorgio, J Hermisson (2019) VolcanoFinder: genomic scans for adaptive introgression. bioRxiv<\/em> doi.org\/10.1101\/697987<\/p>\n\n\n\n[Click to download manual<\/a>]
[Click to download software<\/a>]\n\n\n\n
tar -xzvf volcanofinder_v1.0.tar.gz
Change directory to volcanofinder_v1.0 using a command such as
cd volcanofinder_v1.0
Compile VolcanoFinder<\/em> with the command
make
The VolcanoFinder<\/em> executable will be located in the volvanofinder_v1.0 directory<\/p>\n\n\n\n
March 22, 2019 – Uploaded version 1.0 of the software and manual
March 27, 2019 – Updated software and manual to allow for pre-computed lookup table of probabilities
April 11, 2019 – Updated software and manual to allow for user-defined grid of D<\/em>, and fixed issues with grid of D<\/em> values for Model 2 and issues with blocks
April 12, 2019 – Updated software to fix issue with lower-bound on D<\/em>
July 5, 2019 – Updated software to account for polarization of fixed differences
February 24, 2020 – Updated manual<\/p>\n","protected":false},"excerpt":{"rendered":"