What’s the Answer? (alignment coloring)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is one I’ve heard before from folks in training situations, and that I’ve had to do in the past. If you’ve got a multi-sequence alignment you may want to color code a row or a motif or some feature that you want to indicate that’s different from the default colors you get on MSAs from whatever your source is.

Question: Question about coloring alignment file

Does anyone know how to color some selected columns in an alignment file? For example, how to color column 10, 11, 20 green and column 30 blue? Is there any software available? I do not want to do it by PS. Thanks a lot!


There are several different answers provided, the one I’ve used in the past is the Jalview explanation. If you have other solutions, please be sure to bring them over.