Introduction

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.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.arcadi.navarro@upf.edu.

Publications

  1. SeDuS: segmental duplication simulator.
    Cite this
    Hartasánchez DA, Brasó-Vives M, Fuentes-Díaz J, Vallès-Codina O, Navarro A, 2016-01-01 - Bioinformatics (Oxford, England)
  2. Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario.
    Cite this
    Hartasánchez DA, Vallès-Codina O, Brasó-Vives M, Navarro A, 2014-08-01 - G3 (Bethesda, Md.)

Credits

  1. Diego A Hartasánchez
    Developer

    Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Spain

  2. Marina Brasó-Vives
    Developer

    Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Spain

  3. Juanma Fuentes-Díaz
    Developer

    Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Spain

  4. Oriol Vallès-Codina
    Developer

    Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Spain

  5. Arcadi Navarro
    Investigator

    Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Spain

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Summary
AccessionBT006557
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionSpain
Submitted ByArcadi Navarro