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 -c bioconda 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 or HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI to do multiprocessing
- 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 Emscripten to produce web assembly files, which can be run entirely within a modern browser. See https://observablehq.com/@spond/hyphy-biowasm for an example.
emcmake cmake -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -02 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=["callMain","FS","PROXYFS","WORKERFS","UTF8ToString","getValue","AsciiToString"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT="web,worker" ${EM_FLAGS//-s /-s} -fwasm-exceptions --preload-file res@/hyphy --preload-file tests/hbltests@/tests"
emmake make -j hyphy
This creates
hyphy.js
hyphy.wasm
hyphy.data
Which should be served from the same directory.
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
As noted in the documentation here
hyphy can be run as a command line tool.
Indeed for many analyses the hyphy CLI will return useful
help messages, showing which parameter values can be set to
specify your analysis. For example, running hyphy gard --help
hyphy gard --help
Available analysis command line options
---------------------------------------
Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prompt for its value
[conditionally required] options may or not be required based on the values of other options
type
The type of data to perform screening on
default value: nucleotide
code
Genetic code to use (for codon alignments)
default value: Universal
applies to: Choose Genetic Code
alignment [required]
Sequence alignment to screen for recombination
model
The substitution model to use
default value: JTT
rv
Site to site rate variation
default value: None
max-breakpoints
Maximum number of breakpoints to consider
default value: 10000
rate-classes
How many site rate classes to use
default value: 4
output
Write the resulting JSON to this file (default is to save to the same path as the alignment file + 'GARD.json')
default value: gard.defaultJsonFilePath [computed at run time]
mode
Run mode (Normal or Faster)
default value: Normal
output-lf
Write the best fitting HyPhy analysis snapshot to (default is to save to the same path as the alignment file + 'best-gard')
default value: gard.defaultFitFilePath [computed at run time]
will show you the options that can be set for the gard analysis.
So for instance one could specify a gard run on the command line
with the following command
hyphy gard --alignment /path/to/file --rv GDD --mode Faster --rate-classes 3
While this is a useful feature, it is not always the case that
older analyses will have the same level of support for command line.
For instance, the acd analysis does not have CLI support and
so if one runs the help command
hyphy acd --help
Available analysis command line options
---------------------------------------
Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prompt for its value
[conditionally required] options may or not be required based on the values of other options
No annotated keyword arguments are available for this analysis
one will see that there are no options available. In this case,
you can use a different CLI specification. Indeed the CLI will accept
all of the options that are asked for in an interactive session, as
positional arguments. In this case I could run the acd analysis with
hyphy acd Universal <alignment.fa> MG94CUSTOMCF3X4 Global 012345 <treefile> Estimate
where the options are specified in the exact order that they are asked for in the interactive session. This will work for all hyphy analyses
and provides a less readable but more flexible way to run hyphy analyses.
