What’s the Answer? (black and white MSA figure)

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.

I like to highlight questions at Biostar that solve new problems with visualization. Usually people want to create some kind of figure that explains their work, or some issue from their research, or create a figure like they’ve seen in some source. A lot of times that is not explained in the publications but it could be really helpful for someone.

This week’s highlighted question is one I hadn’t seen before. Someone wanted to reduce the color in a figure. Usually people are asking for more details and complexity, so I thought it was interesting. I can see why someone might want it, but it’s not something I’ve had to do. But there are a couple of good suggestions on this, so if it’s something you could use–there are a couple of ways to accomplish it.

Question: How to color a multiple sequence alignment in black-and-white

sample figure

How could I draw the above figure? I have tried Jalview, bioedit and UGENE but none of them works perfectly. I want to color the figure in black (and/or gray) and white. Is there a software available?

cacaucenturion2

Check out the suggestions in the answers, and add your own thoughts if you have another strategy.