RT Journal Article SR Electronic T1 PHYLUCE is a software package for the analysis of conserved genomic loci JF bioRxiv FD Cold Spring Harbor Laboratory SP 027904 DO 10.1101/027904 A1 Brant C. Faircloth YR 2015 UL http://biorxiv.org/content/early/2015/10/30/027904.abstract AB Summary Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (< 5 Ma to > 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo pre-processing 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.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/fairclothUlab/phyluce/. PHYLUCE is also available as a package (https://binstar.org/fairclothUlab/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.Contact brant{at}fairclothUlab.orgSupplementary information Supplementary Figure 1.