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msprime
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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.

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Requirements
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Msprime requires Python 2.7+ (Python 3 versions are fully supported from
3.1 onwards), the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_
and `HDF5 <https://www.hdfgroup.org/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

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


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

    $ pip install msprime --user

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``.


