title: Constructing linkage maps in the genomics era with MapDisto 2.0.
abstract: BACKGROUND
  Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM).
  
  
  RESULTS
  MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface.
  
  
  METHODS
  The program is available free of charge at mapdisto.free.fr.
  
  
  BACKGROUND
  mapdisto@gmail.com.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Heffelfinger
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Fragoso
authors.affiliation: DIADE Research Unit, Institut de Recherche pour le Développement (IRD), Montpellier, France.|Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia.
authors.forename: Mathias
authors.initials: M
authors.lastname: Lorieux
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D008040:Genetic Linkage; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software