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 is the computational backbone powering datamonkey.org. Additional information is available at hyphy.org.
conda install hyphy
hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>
<method_name>is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)<path_to_alignment_file>is the relative or absolute path to a fasta, nexus or phylib file containing an alignment and tree- A list of the available
<additional_method_specific_arguments>can be seen by runninghyphy <method_name> --help
or
hyphy -i
- cmake >= 3.12
- gcc >= 4.9
- libcurl
- libpthread
- openmp (can be installed on mac via
brew install libomp)
You can download a specific release here or clone this repo with
git clone https://github.com/veg/hyphy.git
Change your directory to the downloaded/cloned directory
cd hyphy
cmake .
make install
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.
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 building on a heterogeneous 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:
- MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") 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)
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
- hyphy 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
Use make test after running cmake ..
Benchmarks, using Github Actions, can be found at http://hyphy.org/bench
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:PATH=/location/of/choice
For example, this configuration will install hyphy at /opt/hyphy
mkdir -p /opt/hyphy
cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/hyphy .
make docs
cd docs
python3 -m http.server