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HyPhy: Hypothesis testing using Phylogenies
C++ HyPhy C Shell Python Makefile Other
Latest commit 2e90ad7 May 5, 2016 @spond spond Merge pull request #431 from stevenweaver/master
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HyPhy - Hypothesis testing using Phylogenies

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HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R.


Hyphy depends on CMake for its build system.

To install, make sure you have CMake >3.0 installed. Hyphy is dependent on other development libraries like libcurl and libpthread. Libcurl requires development libraries such as crypto++ and openssl ( or gnutls depending on your configuration) On Ubuntu these are libcurl-dev, libcrypto++-dev and libssl-dev.

You can download a specific release from this repository or if you prefer the master branch simply clone the repo with

git clone

Change your directory to the newly cloned directory

cd hyphy

Configure the project from the source directory using CMake.

cmake .

If you prefer to use other build systems, such as Xcode, configure using the -G switch

cmake -G Xcode .

CMake supports a number of build system generators, feel free to peruse these and use them if you wish.

By default, HyPhy installs into /usr/local but it can be installed on any location of your system by providing an installation prefix

cmake -DINSTALL_PREFIX=/location/of/choice

For example, this configuration will install hyphy at /opt/hyphy

mkdir -p /opt/hyphy

cmake -DINSTALL_PREFIX=/opt/hyphy .

If you are on an OS X platform, you can specify which OS X SDK to use

cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .

If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run make with one of the following build targets:

  • MAC - build a Mac Carbon application
  • SP - build a HyPhy executable (HYPHYSP) without multiprocessing
  • MP2 - build a HyPhy executable (HYPHYMP) using pthreads to do multiprocessing
  • MPI - build a HyPhy executable (HYPHYMPI) using MPI to do multiprocessing
  • HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI
  • LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing
  • GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)

For example to create a MPI build of HYPHY using openMPI ensure that you have openmpi installed and available on your path. You can check if this is the case after running cmake . you should see something similar to this in your output

-- Found MPI_C: /opt/scyld/openmpi/1.6.3/gnu/lib/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/

-- Found MPI_CXX: /opt/scyld/openmpi/1.6.3/gnu/lib/;/opt/scyld/openmpi/1.6.3/gnu/lib/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/;/usr/lib64/

Then run


And then run make install to install the software

make install

  • HYPHYMP(I) will be installed at /location/of/choice/bin
  • libhyphy_mp.(so/dylib/dll) will be installed at /location/of/choice/lib
  • HyPhy's standard library of batchfiles will go into /location/of/choice/lib/hyphy

HYPHYGTEST isn't installed normally, because it serves no utility outside of testing.

To test HyPhy, build with the GTEST target and run ./HYPHYGTEST from the source directory. make GTEST ./HYPHYGTEST

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