HyPhy - Hypothesis testing using Phylogenies

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.

Quick Start

Install

conda install hyphy

Run with Command Line Arguments

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 running hyphy <method_name> --help

or

Run in Interactive Mode

hyphy -i

Building from Source

Requirements

• cmake >= 3.12
• gcc >= 4.9
• libcurl
• libpthread
• openmp (can be installed on mac via brew install libomp)

Download

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

Build

cmake .

make install

Additional Options for Building from Source

Build Systems

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)

Example (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

• 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

Testing

Use make test after running cmake ..

Benchmarks for CMake Tests

Benchmarks, using Github Actions, can be found at http://hyphy.org/bench

Executable Location

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 .

Building Documentation

make docs
cd docs
python3 -m http.server