Virtual Alignment program?

Question

[maximilian.mayerhofer]

Hello,

I need to do an alignment like in the picture

Is there a way to do that automatically ? Currently, I am using MAFFT to align the sequences and then Jalview to view them - do you know of a program to produce alignments like this?

Best regards

[GenoMax]

If "like this" means looking like this then it is certainly a result of some post-alignment editing. You may have to do the same as well with your MAFFT alignments.

[maximilian.mayerhofer]

Of course, my question is: is there a pipeline/program that can do that for me? Or do I have to do this by hand?