pegi3s/muscle 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 MUSCLE⁠, a sequence alignment tool.

⁠Using the MUSCLE image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/muscle -align /data/sequences.fasta -output /data/sequences_aligned.fasta

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file you want to process.
• sequences.fasta to the actual name of your input file.
• sequences_aligned.fasta to the actual name of your aligned (output) file.

To see the MUSCLE help, just run docker run --rm pegi3s/muscle.

⁠Using the MUSCLE 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/muscle -align /data/sequences.fasta -output /data/sequences_aligned.fasta