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| .. | | 03-May-2022 | - |
| .github/workflows/ | H | 14-Oct-2021 | - | 129 | 116 |
| Examples/ | H | 14-Oct-2021 | - | 6,229 | 3,509 |
| cmake/ | H | 14-Oct-2021 | - | 102 | 91 |
| contrib/ | H | 14-Oct-2021 | - | 156,810 | 92,284 |
| res/ | H | 14-Oct-2021 | - | 125,201 | 106,569 |
| src/ | H | 14-Oct-2021 | - | 119,247 | 78,437 |
| tests/ | H | 14-Oct-2021 | - | 66,084 | 62,530 |
| .coveralls.condarc | H A D | 14-Oct-2021 | 80 | 6 | 5 |
| .coveralls.env.yml | H A D | 14-Oct-2021 | 55 | 5 | 4 |
| .gitattributes | H A D | 14-Oct-2021 | 29 | 2 | 1 |
| .gitignore | H A D | 14-Oct-2021 | 849 | 62 | 53 |
| .travis.yml | H A D | 14-Oct-2021 | 3.7 KiB | 153 | 141 |
| CONTRIBUTING.md | H A D | 14-Oct-2021 | 1.5 KiB | 53 | 28 |
| LICENSE | H A D | 14-Oct-2021 | 1.4 KiB | 35 | 28 |
| README.md | H A D | 14-Oct-2021 | 4.7 KiB | 119 | 71 |
| run_unit_tests.sh | H A D | 14-Oct-2021 | 1.2 KiB | 52 | 34 |
README.md
1[![Build Status](https://travis-ci.org/veg/hyphy.svg?branch=master)](https://travis-ci.org/veg/hyphy)
2
3# HyPhy - Hypothesis testing using Phylogenies
4
5HyPhy 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.
6
7## Quick Start
8
9#### Install
10`conda install hyphy`
11
12#### Run with Command Line Arguments
13`hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>`
14+ _`<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)_
15+ _`<path_to_alignment_file>` is the relative or absolute path to a fasta, nexus or phylib file containing an alignment and tree_
16+ _A list of the available `<additional_method_specific_arguments>` can be seen by running `hyphy <method_name> --help`_
17
18or
19
20#### Run in Interactive Mode
21`hyphy -i`
22
23## Building from Source
24
25#### Requirements
26* cmake >= 3.12
27* gcc >= 4.9
28* libcurl
29* libpthread
30* openmp (can be installed on mac via `brew install libomp`)
31
32#### Download
33You can download a specific release [here](https://github.com/veg/hyphy/releases) or clone this repo with
34
35`git clone https://github.com/veg/hyphy.git`
36
37Change your directory to the downloaded/cloned directory
38
39`cd hyphy`
40
41#### Build
42`cmake .`
43
44`make install`
45
46## Additional Options for Building from Source
47
48#### Build Systems
49If you prefer to use other build systems, such as Xcode, configure using the -G switch
50
51`cmake -G Xcode .`
52
53CMake supports a number of build system generators, feel free to peruse these and use them if you wish.
54
55If you are on an OS X platform, you can specify which OS X SDK to use
56
57`cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .`
58
59If building on a heterogeneous cluster with some nodes that do not support auto-vectorization
60
61`cmake -DNOAVX=ON .`.
62
63If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run `make` with one of the following build targets:
64
65+ MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") using pthreads to do multiprocessing
66+ MPI - build a HyPhy executable (HYPHYMPI) using MPI to do multiprocessing
67+ HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI
68+ LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing
69- GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)
70
71#### Example (MPI build of hyphy using openMPI)
72Ensure 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
73
74`-- 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 `
75
76`-- 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 `
77
78Then run
79
80`make HYPHYMPI`
81
82And then run make install to install the software
83
84`make install`
85
86+ hyphy will be installed at `/location/of/choice/bin`
87+ libhyphy_mp.(so/dylib/dll) will be installed at `/location/of/choice/lib`
88+ HyPhy's standard library of batchfiles will go into `/location/of/choice/lib/hyphy`
89
90
91#### Testing
92
93Use `make test` after running `cmake .`.
94
95#### Benchmarks for CMake Tests
96
97Benchmarks, using Github Actions, can be found at http://hyphy.org/bench
98
99#### Executable Location
100
101By default, HyPhy installs into `/usr/local` but it can be installed on any location of your system by providing an installation prefix
102
103`cmake -DCMAKE_INSTALL_PREFIX:PATH=/location/of/choice`
104
105For example, this configuration will install hyphy at /opt/hyphy
106
107`mkdir -p /opt/hyphy`
108
109`cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/hyphy .`
110
111#### Building Documentation
112
113```
114make docs
115cd docs
116python3 -m http.server
117```
118
119