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forqs

Forward-in-time simulation of Recombination, Quantitative traits, and Selection

forqs image

forqs is a forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. forqs also also models quantitative traits and selection on those traits.

forqs is implemented as a command-line C++ program, using a modular design that gives the user great flexibility in creating custom simulations. It is freely available with a permissive BSD license. You can obtain the latest binary package (Linux, OSX, Windows) from the downloads page.

A manuscript describing forqs has been published in Bioinformatics and is available online (Open Access).

Package contents:

  • bin
    • forqs (the main program)
    • forqs_map_ms (tool for mapping ms coalescent output to forqs output)
  • docs
    • forqs_docs.pdf (main documentation)
    • forqs_module_reference.html (HTML reference for module parameters)
  • examples
    • tutorial_*.txt (tutorials referenced in forqs_docs.pdf)
    • example_*.txt (other examples)

Quick demo:

bin/forqs examples/example_1_locus_selection.txt

Output files will be created in output_example_1_locus_selection


Created by Darren Kessner with John Novembre at UCLA.

Copyright (c) 2013 Regents of the University of California

This software makes use of the Boost C++ libraries

The software also uses the muparser library for parsing mathematical expressions.