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 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.
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.
CONTACT: brant@faircloth-lab.org
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.