SimRA

SimRA (Simulation based on Random-graphs Algorithms) is a software tool to simulate evolutionary scenarios of multiple populations together with subdivisions and admixture. SimRA models coalescence, genetic exchange, and recombination events by producing an Ancestral Recombination Graph (ARG) network structure.

Topic

Genetics;Evolutionary biology;DNA polymorphism;Population genetics

Detail

  • Operation: Modelling and simulation

  • Software interface: Command-line user interface

  • Language: Java

  • License: Apache License v. 2.0

  • Cost: Free

  • Version name: (1.2)

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Laxmi Parida parida@us.ibm.com

  • Collection: -

  • Maturity: Stable

Publications

  • Sampling ARG of multiple populations under complex configurations of subdivision and admixture.
  • Carrieri AP, Utro F, Parida L. Sampling ARG of multiple populations under complex configurations of subdivision and admixture. Bioinformatics. 2016 Apr 1;32(7):1048-56. doi: 10.1093/bioinformatics/btv716. Epub 2015 Dec 7. PMID: 26644417.
  • https://doi.org/10.1093/bioinformatics/btv716
  • PMID: 26644417
  • PMC: -
  • Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.3390/a14050136
  • PMID: -
  • PMC: -

Download and documentation

< Back to DB search