title: DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.
abstract: The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution.
  
  
  
  We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset.
  
  
  
  DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.|Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Frías-López
authors.affiliation: Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: José F
authors.initials: JF
authors.lastname: Sánchez-Herrero
authors.affiliation: Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Guirao-Rico
authors.affiliation: Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain.
authors.forename: Elisa
authors.initials: E
authors.lastname: Mora
authors.affiliation: Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain.
authors.forename: Miquel A
authors.initials: MA
authors.lastname: Arnedo
authors.affiliation: Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sánchez-Gracia
authors.affiliation: Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: Julio
authors.initials: J
authors.lastname: Rozas
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005819:Genetic Markers; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics / Q000379:methods; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D014584:User-Computer Interface
chemical_list: D005819:Genetic Markers