PHYLUCE Is a Software Package for the Analysis of Conserved Genomic Loci

Bioinformatics. 2016 Mar 1;32(5):786-8. doi: 10.1093/bioinformatics/btv646. Epub 2015 Nov 2.


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 PHYLUCE is also available as a package ( 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 and test data are available from doi: 10.6084/m9.figshare.1284521.


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Genetic Loci
  • Genomics
  • Programming Languages
  • Software*

Associated data

  • figshare/10.6084/m9.figshare.1284521