Scripts for simulating coalescents and analysing the output.
The scripts are part of a manuscript currently undergoing peer-review. Citation information will appear in due course.
The example file {codexample.sfs} contains examples for compiling and running the code and generating simulated datapoints and comparing them to data.
Depending on the number of points in the grid of parameter values, the number of trials for each parameter value, and the number of available CPUs, the simulations can take a while, easily several days.
The main requirements are a C++ compiler (e.g. g++ version 8.3.0), Python version 3.7.3, GSL (GNU Scientific Library) version 2.5, the Boost C++ library, and R version 3.6.3 or later.
The code compiles successfully on a Linux Debian 4.19.0-10-amd64 x86-64 architecture. No non-standard hardware is required.
The file {codexample.sfs} contains instructions for compiling the code. Compiling takes only few seconds.
The file {codexample.sfs} contains instructions for compiling and running the code to generate simulated datapoints, and
for further processing the simulated datapoints, e.g. for comparison with actual data.
The expected output is described in the file {codexample.sfs}.
Expected run time varies depending on the specific setup, e.g. the number of grid points in the grid of parameter values, and the number of available CPUs. Running time can, therefore, take from a few minutes to several days.
The file {codexample.sfs} contains instructions for compiling and running the scripts, and for reproducing the output. However, the running time for the results in the manuscript was many days on a powerful computer with 64 CPUs.