{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T10:50:32Z","timestamp":1776682232012,"version":"3.51.2"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T00:00:00Z","timestamp":1578268800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1253710"],"award-info":[{"award-number":["DEB-1253710"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB 1745562"],"award-info":[{"award-number":["DEB 1745562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1557059"],"award-info":[{"award-number":["DEB-1557059"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation","doi-asserted-by":"publisher","award":["BIOTA, 2013\/50297-0"],"award-info":[{"award-number":["BIOTA, 2013\/50297-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Dimensions of Biodiversity Program"},{"name":"Graduate Center of the City University of New York"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>ipyrad is a free and open source tool for assembling and analyzing restriction site-associated DNA sequence datasets using de novo and\/or reference-based approaches. It is designed to be massively scalable to hundreds of taxa and thousands of samples, and can be efficiently parallelized on high performance computing clusters. It is available both as a command line interface and as a Python package with an application programming interface, the latter of which can be used interactively to write complex, reproducible scripts and implement a suite of downstream analysis tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ipyrad is a free and open source program written in Python. Source code is available from the GitHub repository (https:\/\/github.com\/dereneaton\/ipyrad\/), and Linux and MacOS installs are distributed through the conda package manager. Complete documentation, including numerous tutorials, and Jupyter notebooks demonstrating example assemblies and applications of downstream analysis tools are available online: https:\/\/ipyrad.readthedocs.io\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz966","type":"journal-article","created":{"date-parts":[[2019,12,31]],"date-time":"2019-12-31T12:09:55Z","timestamp":1577794195000},"page":"2592-2594","source":"Crossref","is-referenced-by-count":769,"title":["ipyrad: Interactive assembly and analysis of RADseq datasets"],"prefix":"10.1093","volume":"36","author":[{"given":"Deren A R","family":"Eaton","sequence":"first","affiliation":[{"name":"Department of Ecology, Evolution, and Environmental Biology , Columbia University, New York, NY 10027, USA"}]},{"given":"Isaac","family":"Overcast","sequence":"additional","affiliation":[{"name":"Department of Biology, Graduate School, University Center of the City University of New York , New York, NY 10016, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,1,6]]},"reference":[{"key":"2023020108352273100_btz966-B1","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1534\/genetics.111.127324","article-title":"Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication","volume":"188","author":"Amores","year":"2011","journal-title":"Genetics"},{"key":"2023020108352273100_btz966-B2","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrg.2015.28","article-title":"Harnessing the power of RADseq for ecological and evolutionary genomics","volume":"17","author":"Andrews","year":"2016","journal-title":"Nat. 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