SIMCOAL2

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Title SIMCOAL2
Short Description A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models
Long Description We present here SIMCOAL2, an extended version of the SIMCOAL program (Excoffier et al. 2000), to simulate the neutral genetic diversity at partially linked loci under different histories and a wide range of migration and demographic models. SIMCOAL2 includes a number of new features compared to the previous version: The possibility of arbitrary recombination rates between adjacent loci Multiple coalescent events per generation, allowing the correct simulation of very large samples and very large recombining genomic regions The simulation of SNP data with arbitrary minimum frequency, for instance to simulate ascertainment bias The output of diploid genotypic data generated under the assumption of Hardy-Weinberg equilibrium The simulation of a mixture of different data types (DNA sequence, RFLP, STR, or SNP) along a single chromosome.
Version 2.1.2
Project Started 2000
Last Release 14 years, 1 month ago
Homepagehttp://cmpg.unibe.ch/software/simcoal2/
Citations
  • Laval G, Excoffier L, SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history., Bioinformatics, Oct. 12, 2004 [Abstract, cited in PMC ]
  • Excoffier L, Novembre J, Schneider S, SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography., J Hered, Nov. 1, 2000 [Abstract, cited in PMC ]
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