What’s the Answer? (manual MSA editor)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity 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 questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

Manual MSA editor

Does anybody know a good manual editor of multiple sequence alignments. I have been using Genedoc for ages but it really molests me that it doesn’t have an undo function, besides some other small flaws. What is should at least do is insert/remove gaps in a sequence (or in all other sequences), drag, slide, manual editing of residues. Nice would be if has a function to group sequences (and work on the subgroup only). Then it should have all the typical formatting options for publication.

Arjen ten Have

Although there’s no selected answer, there are a number of choices that people offer. Some are well-known and widely used, like JalView. But others may be new to you. Go have a look at all the answers. Or if you have some suggestions, offer them.