On Linux 64-bit, you may use the provided executable

This runs on kernel 2.6.18 and newer:

Otherwise, you must build the executable from source

The source code is available:

Mac: To compile C++ code with the required dependencies, you need XCode and MacPorts:

Install the dependencies:

# Ubuntu
sudo apt-get install build-essential libopenmpi-dev libgsl0-dev

# Mac
#   First, install port (MacPorts):
#   Next, use it to install the dependencies:
sudo port selfupdate && sudo port install gcc48 openmpi gsl

# Broad Institute
#   Add this line to ~/.my.bashrc or ~/.my.cshrc
use .gcc-4.8.1 .openmpi-1.4 .gsl-1.14

Download and compile the code:

#   Clone with git; easily get updates with 'git pull':
git clone
cd snpsea

#   If you don't have git:
curl -LOk
unzip; cd snpsea-master

cd src; make               #   Compile.
cp ../bin/snpsea* ~/bin/   #   Copy the executables wherever you like.

C++ Libraries

To compile SNPsea, you will need a modern C++ compiler that supports c++0x and the dependencies listed below. I compiled successfully with gcc versions 4.6.3 (the default version for Ubuntu 12.04) and 4.8.1.


a minimal C++ interval tree implementation


Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.


MPI is a standardized API typically used for parallel and/or distributed computing. Open MPI is an open source, freely available implementation.

GSL - GNU Scientific Library

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.

GCC, the GNU Compiler

The GNU Compiler Collection is a compiler system produced by the GNU Project supporting various programming languages.

Python Packages

To plot visualizations of the results, you will need Python 2.7 and the packages listed below.

Instructions: Install with pip:

pip install docopt numpy pandas matplotlib

Note: The packages available on the Ubuntu repositories may be outdated and might fail to work. So, avoid using apt-get for these dependencies.


Command-line interface description language.


NumPy is the fundamental package for scientific computing with Python.


pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.


matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

Note: On a server with no display, please edit your matplotlibrc file to use the Agg backend:

perl -i -pe 's/^(\s*(backend).*)$/#$1\n$2:Agg/' ~/.matplotlib/matplotlibrc

Otherwise, you may see an error message like this:

_tkinter.TclError: no display name and no $DISPLAY environment variable

R Packages

Some visualizations use R and ggplot2 instead of Python and matplotlib.

Instructions: Start a session in R and run:

install.packages(c("data.table", "reshape2", "gap", "ggplot2"))


Extension of data.frame for fast indexing, fast ordered joins, fast assignment, fast grouping and list columns.


Flexibly reshape data: a reboot of the reshape package.


Genetic analysis package.


An implementation of the Grammar of Graphics.