This page contains various coalescent simulations that we
have written. These simulations make heavy use of two
libraries, libsequence and the GNU Scientific Library. You will need
those packages to be installed on your system before
attempting to compile the software on this page. Note
that the GSL is not our project, so any questions
about that should be directed to their mailing lists.
Please remember to cite the relevant papers listed below if
you use any of these packages for your research.
Simulation code from Thornton (2007)
The neutral coalescent process for recent gene
duplications and copy-number variants. Genetics 177:
987-1000
Simulation code from
Thornton and Jensen (2007) Controlling the
false-positive rate in multilocus genome scans for
selection. Genetics 175: 737-750
This code simulates a sweep in a bottlenecked population,
plus the ancestral population. See paper for details.
Simulation
code for models of recurrent hitch-hlking used in
Jensen, Thornton and Andolfatto (2008) PLoS Genetics