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This archive contains code to perform the likelihood calculations described in Terhorst, Schlötterer & Song (2015).

Compilation Instructions

There are two dependencies required to build this package which are not standard on all UNIX-like systems:

  • A C++11-compliant compiler (such as GCC 4.8 or higher). The clang compiler shipped with recent versions of Mac OS X should also work.

  • The google-sparsehash library (https://code.google.com/p/sparsehash/).

To compile the package, type make in the directory containing this README file.

Usage Instructions

The file example.py is example of how to use this library to perform inference. It analyzes a test data set (also included) in order to test for and estimate selection. Refer to the comments in that file for further details. Execute example.py using the wrapper script example.sh in order to ensure that the threelocus library can be located on your system's library path.

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Multi-locus analysis of evolve-and-resequence time series data.

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