msprime 0.1.1a4

A fast and accurate coalescent simulator.

Msprime is a reimplementation of Hudson’s classical ms program for modern datasets. It is under heavy development at the moment, and the present code should be considered beta quality. Bugs may be present, and the API might change considerably. We provide an ms-compatible command line interface mspms, which should be useful to fit into existing workflows. However, the Python API is the recommended way to use msprime to gain full advantage of its internal structures.

Full documentation is forthcoming.

Requirements

Msprime requires Python 2.7+ (Python 3 versions are fully supported from 3.1 onwards), the GNU Scientific Library and HDF5, which are available for all major platforms. For example, to install on Debian/Ubuntu use:

# apt-get install python-dev libgsl0-dev libhdf5-serial-dev pkg-config

TODO

• Need installation instructions for an RPM based distribution, HomeBrew/MacPorts and possibly a linux distro where we are missing root access.

Installation

The simplest method of installation is to use PyPI and pip:

$ pip install msprime --user --pre

will install msprime your user Python installation. This should work in most cases (but see the Requirements section).

To use the ms-compatible command line program, you must ensure that the ~/.local/bin/ directory is in your PATH.