pegi3s/jaligner 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 JAligner⁠, a pairwise sequence alignment tool.

⁠Using the JAligner image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/jaligner /data/fastaFile1 /data/fastaFile2 EDNAFULL 10 1

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file(s).
• fastaFile1 to the actual name of your first input FASTA file.
• fastaFile2 to the actual name of your second input FASTA file.
• EDNAFULL to the actual name of your scoring matrix (e.g. BLOSUM62 for proteins).
• 10 to the actual open gap penalty.
• 1 to the actual extend gap penalty.