msParSm

The msParSm application is an evolution of msPar ⁽¹⁾, the parallel version of the coalescent simulation program ms ⁽²⁾, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence.

Pre-requisites

• Linux GNU Compiler 4.9.1 (or greater)
• OpenMPI 1.10.1 (other releases in the branch 1.10 should be fine)
  • Version 1.8.x could potentially be fine, but please notice that msParSm was not fully tested with such version.
• CMake 3.5.1 (or greather) OR GNU Make 3.81 (or greater)

How to Build

There are two ways for building msParSm: CMake and Make. If you have installed CMAKE with version greater than 3.5.0, then go with CMake, otherwise you should use Make.

CMake

cmake <src-path> -DCMAKE_INSTALL_PREFIX=<install-path>

Make

make install

Binary files will be put into the bin folder (which is already git ignored).

How to Use

Usage is the mostly the same as with traditional ms, but you need to run it through OpenMPI. Next example will run the application using 4 threads:

mpirun -n 4 bin/msparsm 10 20 -seeds 40328 19150 54118 -t 100 -r 100 100000 -I 2 2 8 -eN 0.4 10.01 -eN 1 0.01 -en 0.25 2 0.2 -ej 3 2 1 -T > results.out