PHYLUCE is a software package for the analysis of conserved genomic loci

Abstract

SummaryTargeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales ( 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.\n\nAvailability and ImplementationPHYLUCE 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.\n\nContactbrant@fairclothUlab.org\n\nSupplementary informationSupplementary Figure 1.\n\nO_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC=\"FIGDIR/small/027904_figS1.gif\" ALT=\"Figure 1\">\nView larger version (40K):\norg.highwire.dtl.DTLVardef@1f6fb2aorg.highwire.dtl.DTLVardef@1e39afforg.highwire.dtl.DTLVardef@1d51cf1org.highwire.dtl.DTLVardef@5f2eda_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 1.C_FLOATNO PHYLUCE workflow for phylogenomic analyses of data collected from conserved genomic loci using targeted enrichment.\n\nC_FIG