SeDuS: segmental duplication simulator

Hartasánchez Frenk, Diego Andrés, 1982-; Brasó-Vives, Marina, 1990-; Fuentes-Díaz, Juanma; Vallés-Codina, Oriol; Navarro i Cuartiellas, Arcadi, 1969-

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dc.contributor.author	Hartasánchez Frenk, Diego Andrés, 1982-
dc.contributor.author	Brasó-Vives, Marina, 1990-
dc.contributor.author	Fuentes-Díaz, Juanma
dc.contributor.author	Vallés-Codina, Oriol
dc.contributor.author	Navarro i Cuartiellas, Arcadi, 1969-
dc.date.accessioned	2017-05-22T11:24:24Z
dc.date.available	2017-05-22T11:24:24Z
dc.date.issued	2016
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.issn	1367-4803
dc.identifier.uri	http://hdl.handle.net/10230/32140
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/pdf
dc.language.iso	eng
dc.publisher	Oxford University Press
dc.relation.ispartof	Bioinformatics. 2016 Jan 1;32(1):148-50
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.subject.other	Àcids nucleics
dc.subject.other	Simulació per ordinador
dc.subject.other	Evolució molecular
dc.title	SeDuS: segmental duplication simulator
dc.type	info:eu-repo/semantics/article
dc.identifier.doi	http://dx.doi.org/10.1093/bioinformatics/btv481
dc.relation.projectID	info:eu-repo/grantAgreement/ES/3PN/BFU2012-38236
dc.rights.accessRights	info:eu-repo/semantics/openAccess
dc.type.version	info:eu-repo/semantics/acceptedVersion