{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T02:52:14Z","timestamp":1786157534701,"version":"3.56.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (&amp;lt;5\u2009Ma to\u00a0&amp;gt; 300\u2009Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.<\/jats:p>\n                  <jats:p>Availability and Implementation: PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat\/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from https:\/\/www.github.com\/faircloth-lab\/phyluce\/. PHYLUCE is also available as a package (https:\/\/binstar.org\/faircloth-lab\/phyluce) for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from http:\/\/phyluce.readthedocs.org\/en\/latest\/ and test data are available from doi: 10.6084\/m9.figshare.1284521.<\/jats:p>\n                  <jats:p>Contact: \u00a0brant@faircloth-lab.org<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv646","type":"journal-article","created":{"date-parts":[[2015,11,3]],"date-time":"2015-11-03T20:43:32Z","timestamp":1446583412000},"page":"786-788","source":"Crossref","is-referenced-by-count":971,"title":["PHYLUCE is a software package for the analysis of conserved genomic loci"],"prefix":"10.1093","volume":"32","author":[{"given":"Brant C.","family":"Faircloth","sequence":"first","affiliation":[{"name":"Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,11,2]]},"reference":[{"key":"2023020110451198600_btv646-B1","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1093\/molbev\/msu236","article-title":"ExaBayes: massively parallel bayesian tree inference for the whole-genome era","volume":"31","author":"Aberer","year":"2014","journal-title":"Mol. 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