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reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","c-plus-plus","comparative-genomics","evolution","phylogenetics","science","statistical-methods"],"created_at":"2025-02-10T22:35:20.831Z","updated_at":"2026-02-28T00:18:23.629Z","avatar_url":"https://github.com/veg.png","language":"HyPhy","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hyphy/README.html)\n![https://anaconda.org/bioconda/hyphy/badges/version.svg](https://anaconda.org/bioconda/hyphy/badges/version.svg)\n![https://anaconda.org/bioconda/hyphy/badges/latest_release_date.svg](https://anaconda.org/bioconda/hyphy/badges/latest_release_date.svg)\n![https://anaconda.org/bioconda/hyphy/badges/downloads.svg](https://anaconda.org/bioconda/hyphy/badges/downloads.svg)\n\n# HyPhy - Hypothesis testing using Phylogenies\n\nHyPhy 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.\n\n## Quick Start\n\n#### Install\n`conda install -c bioconda hyphy`\n\n#### Running with Docker\nYou can also run HyPhy without having to install it on your system using the provided Dockerfile. Following the below instructions starts an interactive Docker container where HyPhy is already available. \n\nIf you don't have Docker installed, first look at [Docker Desktop](https://docs.docker.com/desktop/).\n\n**Please note you must change this code snippet to point to the appropriate location for your input data. This will be made available inside the container at `/hyphy/data`.**\n\n```\ngit clone https://github.com/veg/hyphy.git\ncd hyphy\ndocker build -t hyphy:latest .\ndocker run --rm -v [path-to-your-input-data]:/hyphy/data -it hyphy:latest\n```\n\n#### Run with Command Line Arguments\n`hyphy \u003cmethod_name\u003e --alignment \u003cpath_to_alignment_file\u003e \u003cadditional_method_specific_arguments\u003e`  \n+ _`\u003cmethod_name\u003e` is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)_\n+ _`\u003cpath_to_alignment_file\u003e` is the relative or absolute path to a `FASTA`, `NEXUS`, `Phylip`, or `MEGA` file containing an alignment and tree_\n+ _A list of the available `\u003cadditional_method_specific_arguments\u003e` can be seen by running `hyphy \u003cmethod_name\u003e --help`_\n\nor  \n\n#### Run in Interactive Mode\n`hyphy -i`  \n\n## Building from Source\n\n#### Requirements\n* cmake \u003e= 3.12\n* gcc \u003e= 4.9\n* libcurl\n* libpthread\n* openmp (can be installed on mac via `brew install libomp`)\n\n#### Download\nYou can download a specific release [here](https://github.com/veg/hyphy/releases) or clone this repo with\n\n`git clone https://github.com/veg/hyphy.git`\n\nChange your directory to the downloaded/cloned directory\n\n`cd hyphy`\n\n#### Build\n`cmake .`\n\n`make install`\n\n## Additional Options for Building from Source\n\n#### Build Systems\nIf you prefer to use other build systems, such as Xcode, configure using the -G switch\n\n`cmake -G Xcode .`\n\nCMake supports a number of build system generators, feel free to peruse these and use them if you wish.\n\nIf you are on an OS X platform, you can specify which OS X SDK to use\n\n`cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .`\n\nIf building on a heterogeneous cluster with some nodes that do not support auto-vectorization  \n\n`cmake -DNOAVX=ON .`.\n\nIf you're on a UNIX-compatible system, and you're comfortable with GNU make, then run `make` with one of the following build targets:\n\n+   MP or hyphy - build a HyPhy executable (This used to be \"HYPHYMP\" but is now just \"hyphy\") using pthreads to do multiprocessing\n+   MPI or HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI to do multiprocessing\n+   LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing\n-   GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)\n\n#### Example (MPI build of hyphy using openMPI)\nEnsure 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\n\n`-- 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 `\n\n`-- 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 `\n\nThen run \n\n`make HYPHYMPI`\n\nAnd then run make install to install the software\n\n`make install`\n\n+   hyphy will be installed at  `/location/of/choice/bin`\n+   libhyphy_mp.(so/dylib/dll) will be installed at `/location/of/choice/lib`\n+   HyPhy's standard library of batchfiles will go into `/location/of/choice/lib/hyphy`\n\n#### WebAssembly Build\n\nHyPhy provides WebAssembly builds that can run in modern browsers without installation.\n\n##### Using Pre-built WebAssembly Files\n\nThe latest WebAssembly build can be downloaded from the GitHub Actions artifacts. Go to the [GitHub Actions page](https://github.com/veg/hyphy/actions/workflows/wasm-build.yml), select the most recent successful workflow run, and download the `hyphy-wasm` artifact. The artifact contains:\n\n```\nhyphy.js\nhyphy.wasm\nhyphy.data\nhyphy_resources.tar.gz\n```\n\nExtract the resources tarball (`hyphy_resources.tar.gz`) in the same directory as the other files. All files should be served from the same directory on your web server. For an example of HyPhy running in the browser, see https://observablehq.com/@spond/hyphy-biowasm.\n\n##### Building WebAssembly Files Locally\n\nTo build the WebAssembly files yourself, you'll need [Emscripten](https://emscripten.org/docs/compiling/Building-Projects.html).\n\n1. Configure the build - note that we don't use preload flags during configuration to avoid CMake test issues:\n```\nemcmake cmake -DCMAKE_EXE_LINKER_FLAGS=\"-sTOTAL_STACK=2097152 -O2 -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\"\n``` \n\n2. Build the target:\n```\nemmake make -j hyphy \n```\n\n3. This will create the following files:\n```\nhyphy.js\nhyphy.wasm\nhyphy.data\n```\n\n4. You'll also need to copy the resource files to serve alongside the WebAssembly files:\n```\nmkdir -p hyphy_resources\ncp -r res hyphy_resources/\ncp -r tests/hbltests hyphy_resources/tests\n```\n\n5. All files should be served from the same directory on your web server.\n\n#### Testing\n\nUse `make test` after running `cmake .`.\n\n#### Benchmarks for CMake Tests\n\nBenchmarks, using Github Actions, can be found at http://hyphy.org/bench\n\n#### Executable Location\n\nBy default, HyPhy installs into `/usr/local` but it can be installed on any location of your system by providing an installation prefix\n\n`cmake -DCMAKE_INSTALL_PREFIX:PATH=/location/of/choice`\n\nFor example, this configuration will install hyphy at /opt/hyphy\n\n`mkdir -p /opt/hyphy`\n\n`cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/hyphy .`\n\n#### Building Documentation\n\n```\nmake docs\ncd docs\npython3 -m http.server\n```\n\n## CLI notes\n\nAs noted in the documentation [here](http://www.hyphy.org/tutorials/CLI-tutorial/) \n`hyphy` can be run as a command line tool.\nIndeed for many analyses the `hyphy` CLI will return useful \nhelp messages, showing which parameter values can be set to \nspecify your analysis. For example, running `hyphy gard --help`\n\n```{bash}\nhyphy gard --help \n\nAvailable analysis command line options\n---------------------------------------\nUse --option VALUE syntax to invoke\nIf a [reqired] option is not provided on the command line, the analysis will prompt for its value\n[conditionally required] options may or not be required based on the values of other options\n\ntype\n\tThe type of data to perform screening on\n\tdefault value: nucleotide\n\ncode\n\tGenetic code to use (for codon alignments)\n\tdefault value: Universal\n\tapplies to: Choose Genetic Code\n\nalignment [required]\n\tSequence alignment to screen for recombination\n\nmodel\n\tThe substitution model to use\n\tdefault value: JTT\n\nrv\n\tSite to site rate variation\n\tdefault value: None\n\nmax-breakpoints\n\tMaximum number of breakpoints to consider\n\tdefault value: 10000\n\nrate-classes\n\tHow many site rate classes to use\n\tdefault value: 4\n\noutput\n\tWrite the resulting JSON to this file (default is to save to the same path as the alignment file + 'GARD.json')\n\tdefault value: gard.defaultJsonFilePath [computed at run time]\n\nmode\n\tRun mode (Normal or Faster)\n\tdefault value: Normal\n\noutput-lf\n\tWrite the best fitting HyPhy analysis snapshot to (default is to save to the same path as the alignment file + 'best-gard')\n\tdefault value: gard.defaultFitFilePath [computed at run time]\n```\n\nwill show you the options that can be set for the `gard` analysis.\nSo for instance one could specify a `gard` run on the command line\nwith the following command\n\n```{bash}\nhyphy gard --alignment /path/to/file --rv GDD --mode Faster --rate-classes 3\n```\n\nWhile this is a useful feature, it is not always the case that \nolder analyses will have the same level of support for command line.\nFor instance, the `acd` analysis does not have CLI support and \nso if one runs the help command\n\n```{bash}\nhyphy acd --help \n\nAvailable analysis command line options\n---------------------------------------\nUse --option VALUE syntax to invoke\nIf a [reqired] option is not provided on the command line, the analysis will prompt for its value\n[conditionally required] options may or not be required based on the values of other options\n\nNo annotated keyword arguments are available for this analysis\n```\n\none will see that there are no options available. 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