title: PhyDesign: an online application for profiling phylogenetic informativeness.
abstract: BACKGROUND
  The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available.
  
  
  RESULTS
  Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.
  
  
  CONCLUSIONS
  By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA. francesc.lopez@gmail.com
authors.forename: Francesc
authors.initials: F
authors.lastname: López-Giráldez
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Townsend
mesh_terms: D030541:Databases, Genetic; D056426:Genetic Loci; D010802:Phylogeny; D012984:Software