{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T18:37:57Z","timestamp":1760985477159},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,26]],"date-time":"2016-10-26T00:00:00Z","timestamp":1477440000000},"content-version":"vor","delay-in-days":132,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In an attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters\/data for phylogenetic inference, we introduce the perl pipeline RADIS. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample\/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci\/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilized.<\/jats:p><jats:p>Availability and implementation: RADIS is written in perl, designed to run on Linux and Unix platforms. RADIS and its manual are freely available from http:\/\/www1.montpellier.inra.fr\/CBGP\/software\/RADIS\/.<\/jats:p><jats:p>Contact: \u00a0astrid.cruaud@supagro.inra.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw352","type":"journal-article","created":{"date-parts":[[2016,6,17]],"date-time":"2016-06-17T01:28:17Z","timestamp":1466126897000},"page":"3027-3028","source":"Crossref","is-referenced-by-count":15,"title":["<i>RADIS:<\/i>analysis of<i>RAD<\/i>-seq data for interspecific phylogeny"],"prefix":"10.1093","volume":"32","author":[{"given":"Astrid","family":"Cruaud","sequence":"first","affiliation":[{"name":"1 INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathieu","family":"Gautier","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France,"},{"name":"2 IBC, F-34095 Montpellier, France,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Pierre","family":"Rossi","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Yves","family":"Rasplus","sequence":"additional","affiliation":[{"name":"1 INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00e9r\u00f4me","family":"Gouzy","sequence":"additional","affiliation":[{"name":"3 INRA, UMR441 LIPM, F31326 Castanet Tolosan, France"},{"name":"4 CNRS, UMR2594 LIPM, F31326 Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,16]]},"reference":[{"key":"2023020113463679500_btw352-B1","doi-asserted-by":"crossref","first-page":"e3376","DOI":"10.1371\/journal.pone.0003376","article-title":"Rapid SNP discovery and genetic mapping using sequenced RAD markers","volume":"3","author":"Baird","year":"2008","journal-title":"PLoS ONE"},{"key":"2023020113463679500_btw352-B2","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1111\/mec.12354","article-title":"Stacks: an analysis tool set for population genomics","volume":"22","author":"Catchen","year":"2013","journal-title":"Mol. 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