Journal
BIOINFORMATICS
Volume 32, Issue 5, Pages 786-788Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv646
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Funding
- National Science Foundation Division of Environmental Biology [DEB-1242260, DEB-0956069, DEB-0841729, DEB-1354739]
- Louisiana State University
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Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (< 5Ma 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.
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