What’s the Answer? (alignment editors)

PuzzledThis week’s highlighted question is from the Bioinformatics discussion area at Reddit. There are a range of topics discussed in that subreddit, and some of the tool-specific ones are very helpful in learning about new software.

What are some of the best multiple alignment editors that allow for manual editing?

Cross-platform/open-source would be preferred.


There were tools I am familiar with (JalView is the one I have used the most), but I learned about a new tool that looked useful as well. AliView. It sounds as if they have provided a nice tool that manages large datasets better than existing software. As they describe it on their site:

“AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use, not so bloated and hopefully to your liking.”

Heh. Not bloated.

Anyway, looks like it may be worth kicking the tires a bit. In the paper they note that it was related to the 1000 Plants (1kp or OneKP) project “while designing degenerate primers for a diverse set of ferns from transcriptome data”. Anders Larsson talks about the what was needed for this work, and it seems like these needs are going to be common among a lot of folks doing these kinds of large-scale sequencing projects with new species. So I can see this utility of this, and would encourage folks to have a look at AliView.

Quick links:

JalView: http://www.jalview.org/

AliView: http://www.ormbunkar.se/aliview/


Larsson A. (2014). AliView: a fast and lightweight alignment viewer and editor for large datasets, Bioinformatics, 30 (22) 3276-3278. DOI: http://dx.doi.org/10.1093/bioinformatics/btu531