Using HyPhy as a standard command line tool#
As of version 2.4.0 HyPhy is a bonified command line tool.
An executable with key-word arguments, relative paths to files and sane defaults.
The interactive command line prompt is still avaialible if you prefer that (simply run
This page provides some general information about using HyPhy as a command line tool; the older command line prompt tutorial provides more details about each method.
Like any command line tool, to see the available options simply run
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 you're tree is in a seperate file (not the same file as the alignment) add a
hyphy slac --alignment CD2.fasta --tree CD2.newick
Most methods require only an alignment and a tree.
Default values are used for any other options.
To see a list of the available options for a method run
hyphy <method_name> --help (
hyphy slac --help in our example).
Key word arguments and interactive prompts can be mixed by including
-i before any key word arguments.
hyphy -i slac --alignment CD2.fasta --code Universal
Will begin a slac analysis with CD2.fasta using the universal genetic code and prompt you for all the non-specified options: a tree file, branch selection, number of samples for ancesteral state reconstruction, p-value.
Markdown formatted status indicators will be printed to stdout as the analysis runs.
Final results will be saved in a JSON-formatted file (saved in the same directory as the alignment file unless a
--output argument is provided). This JSON results file can be uploaded at vision.hyphy.org for an interactive visualization of the results.
To see a list of the methods that can be run with a command line invocation run