title: HyPhy: hypothesis testing using phylogenies.
abstract: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
  
  
  BACKGROUND
  http://www.hyphy.org
  
  
  BACKGROUND
  muse@stat.ncsu.edu
  
  
  BACKGROUND
  HyPhydocumentation and tutorials are available at http://www.hyphy.org.
authors.affiliation: Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA.
authors.forename: Sergei L Kosakovsky
authors.initials: SL
authors.lastname: Pond
authors.forename: Simon D W
authors.initials: SD
authors.lastname: Frost
authors.forename: Spencer V
authors.initials: SV
authors.lastname: Muse
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface