Versions: [3.8.1551]


Download        : docker pull
Compressed Size : 27MB


MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.


Pull (Download)

To download the latest version of muscle run,

docker pull

or to download a specific version of muscle run,

docker pull


To run the container as an application run,

docker run --rm muscle --version

or to run the container in an interactive session run,

docker run -it --rm bash

Mounting volumes between the container and your machine

To access files from your machine within the muscle container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data muscle /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.


If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC muscle container here.