pegi3s/hyphy repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of HyPhy⁠ (Hypothesis Testing using Phylogenies), an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution and machine learning.

Starting with HyPhy 2.5, analyses are run through the hyphy executable. The available standard analyses include absrel, bgm, busted, fade, fel, fubar, gard, meme, relax and slac.

⁠Using the HyPhy image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/hyphy hyphy <analysis> --alignment /data/inputFile --output /data/output/out.json

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <analysis> to the name of the analysis you want to run (e.g. fel, fubar).
• inputFile to the actual name of your input alignment file.
• out.json to the actual name of your output file.

To list the available analyses and their options, run docker run --rm pegi3s/hyphy hyphy -h and docker run --rm pegi3s/hyphy hyphy <analysis> --help. HyPhy also provides an interactive mode: docker run --rm -it pegi3s/hyphy hyphy -i.

⁠Test data

To test the previous command, you can use the example datasets provided here⁠. After uncompressing the downloaded file, you should replace /your/data/dir by the actual working directory and run, for example:

docker run --rm -v /your/data/dir:/data pegi3s/hyphy hyphy fel --alignment /data/tutorial_data/lysin.fna --output /data/out.json

In the end, a JSON file with the results is generated.

⁠Using the HyPhy image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/hyphy hyphy <analysis> --alignment /data/inputFile --output /data/output/out.json