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.
- cmake >= 3.0
- gcc >= 4.9
- libcurl
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 https://github.com/veg/hyphy.git
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 -DCMAKE_INSTALL_PREFIX=/location/of/choice
For example, this configuration will install hyphy at /opt/hyphy
mkdir -p /opt/hyphy
cmake -DCMAKE_INSTALL_PREFIX=/opt/hyphy .
If building on a hetereogenous cluster with some nodes that do not support auto-vectorization
cmake -DNOAVX=ON ..
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
- HYPHYGTK - HYPHY with GTK
- SP - build a HyPhy executable (HYPHYSP) without multiprocessing
- MP - 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/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so
-- Found MPI_CXX: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi_cxx.so;/opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so
Then run
`make HYPHYMPI`
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