SeDuS: segmental duplication simulator

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  • dc.contributor.author Hartasánchez Frenk, Diego Andrés, 1982-ca
  • dc.contributor.author Brasó-Vives, Marina, 1990-ca
  • dc.contributor.author Fuentes-Díaz, Juanmaca
  • dc.contributor.author Vallés-Codina, Oriolca
  • dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-ca
  • dc.date.accessioned 2017-05-22T11:24:24Z
  • dc.date.available 2017-05-22T11:24:24Z
  • dc.date.issued 2016
  • dc.description.abstract SUMMARY: SeDuS is the first flexible and user-friendly forward-in-time simulator of patterns of molecular evolution within segmental duplications undergoing interlocus gene conversion and crossover. SeDuS introduces known features of interlocus gene conversion such as biased directionality and dependence on local sequence identity. Additionally, it includes aspects such as different selective pressures acting upon copy number and flexible crossover distributions. A graphical user interface allows fast fine-tuning of relevant parameters and straightforward real-time analysis of the evolution of duplicates. AVAILABILITY AND IMPLEMENTATION: SeDuS is implemented in C++ and can be run via command line or through a graphical user interface developed using Qt C++. Source code and binary executables for Linux, OS X and Windows are freely available at www.biologiaevolutiva.org/sedus/. A tutorial with a detailed description of implementation, parameters and output files is available online.
  • dc.description.sponsorship This work was supported by the Spanish National Institute of Bioinformatics, a platform of the Instituto de Salud Carlos III (PT13/0001/0026), and the Spanish Government, Grant BFU2012-38236 to A.N.; by grants to D.A.H. from Conacyt and CSIC (JAE Predoc); by the Fondo Europeo de Desarrollo Regional (FEDER) and the Fondo Social Europeo (FSE) and by a grant to M.B.-V. from AGAUR (FI – DGR 2015)
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Hartasánchez DA, Brasó-Vives M, Fuentes-Díaz J, Vallès-Codina O1, Navarro A. SeDuS: segmental duplication simulator. Bioinformatics. 2016 Jan 1;32(1):148-50. DOI: 10.1093/bioinformatics/btv481
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btv481
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/32140
  • dc.language.iso eng
  • dc.publisher Oxford University Pressca
  • dc.relation.ispartof Bioinformatics. 2016 Jan 1;32(1):148-50
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2012-38236
  • dc.rights © Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version Hartasánchez DA, Brasó-Vives M, Fuentes-Díaz J, Vallès-Codina O1, Navarro A. SeDuS: segmental duplication simulator. Bioinformatics. 2016 Jan 1; 32(1): 148-50 is available online at: http://dx.doi.org/10.1093/bioinformatics/btv481
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.subject.other Àcids nucleics
  • dc.subject.other Simulació per ordinador
  • dc.subject.other Evolució molecular
  • dc.title SeDuS: segmental duplication simulatorca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/acceptedVersion

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