SeDuS: segmental duplication simulator.
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. CONTACT: firstname.lastname@example.org.
Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, 08003. Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, 08003, National Institute for Bioinformatics, 08003, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 and Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain.