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Like any command line tool, to see the available options simply run hyphy --help. Once you've installed hyphy run the method of your choice like so (we'll use SLAC for demonstration purposes): hyphy slac --alignment CD2.nex. If your tree is in a separate file (not the same file as the alignment) add a --tree flag. hyphy slac --alignment CD2 ...
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Please take your time to fill out all the relevant...
- Methods
Information, documentation, and news about the HyPhy...
- Resources
Tutorials for using standard methods in HyPhy to infer...
- Installation
HyPhy can be built in two main flavors: Multi-threaded,...
- About
Overview#. HyPhy (Hypothesis Testing using Phylogenies) is...
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- HyPhy - Hypothesis testing using Phylogenies
- Quick Start
- Building from Source
- Additional Options for Building from Source
- CLI notes
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 environm...
Install
conda install hyphy
Run with Command Line Arguments
hyphy --alignment
• is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)
• is the relative or absolute path to a fasta, nexus or phylib file containing an alignment and tree
Requirements
•cmake >= 3.12
•gcc >= 4.9
•libcurl
•libpthread
•openmp (can be installed on mac via brew install libomp)
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/ .
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
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
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
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
This option is the most flexible approach through which you can access all available analyses and pipelines as well as customize your own HyPhy analyses. Follow these instructions for download and installation. HyPhy can be run from the command line in two ways: Standard command line tool: additional information available here
Aug 27, 2019 · HyPhy can be run on a desktop, either as a command-line tool for access to its complete functionality, or via a simple Electron-based graphical user interface to access the most popular analyses. Computing cluster use and pipeline integration is facilitated via flexible specification of command line arguments.
- Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Ben Murrell, ...
- 10.1093/molbev/msz197
- 2020
- Mol Biol Evol. 2020 Jan; 37(1): 295-299.
Launch HyPhy from the command line by entering HYPHYMP. Provide the following options to the menu prompts: Enter 10 to select Positive Selection. Enter 4 to select Run the Branch-site Unrestricted Statistical Test for Episodic Diversification to test for evidence of episodic alignment-wide selective pressure.
Jul 26, 2023 · This is done because HyPhy needs to be able to create parameter names like tree.node.parameter where node is a sequence name for leaf nodes. If node has spaces, arithmetic operation symbols, etc, this will lead to run-time errors. 1 or TRUE (default): convert all sequence names to valid HyPhy identifiers.
People also ask
Can hyphy be run as a command line tool?
How do I use hyphy?
How do I test hyphy V3?
Which hyphy method should I use?
Launch HyPhy from the command line by typing hyphy -i. Navigate through the prompt to reach the aBSREL analysis: Enter 1 for "Selection Analyses", and then 6 for "aBSREL". Respond to the following prompts: Choose Genetic Code: Enter 1 to select the Universal genetic code.
