pegi3s/mafft 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 MAFFT⁠, a multiple sequence alignment tool that offers a range of multiple alignment methods like L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences) and so on.

⁠Using MAFFT image in Linux

In order to use this image you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/mafft bash -c "mafft /data/sequences.fasta > /data/sequences_aligned.fasta"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTA file you want to align.
• sequences.fasta to the actual name of your FASTA file.
• sequences_aligned.fasta to the actual name of your aligned FASTA file.

To see the MAFFT help, just run docker run --rm pegi3s/mafft mafft --help.

⁠Test data

To test the previous command, you can copy and paste the following sample data into the sequences.fasta file:

>Sequence1
AAAAAAAATTTTTTTT
>Sequence2
AAAAAATTTTTT
>Sequence3
AAAATTTT

⁠Using MAFFT 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/mafft bash -c "mafft /data/sequences.fasta > /data/sequences_aligned.fasta"