publication . Preprint . Article . Other literature type . 2015

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

Faircloth, Brant C;
Open Access
  • Published: 01 Oct 2015
  • Publisher: Cold Spring Harbor Laboratory
Abstract
UNLABELLED: Targeted 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 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...
Funded by
NSF| Collaborative Research: EAGER: Using ultraconserved elements (UCEs) as genomic markers to study shallow levels of evolutionary divergence
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1242260
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| EAGER: Developing bioinformatics tools for the application of next-generation sequencing technologies to phylogeography.
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0956069
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NSF| Comparative phylogeography of Neotropical birds with cross-Andes distributions
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0841729
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| Collaborative Research: Ant Diversity of the MesoAmerican Corridor (ADMAC)
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1354739
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
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