Visualizing differences between alternative multiple sequence alignments of the same dataset
Java Other
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


AlignmentComparator is a desktop application that visualizes differences between two alternative multiple sequence alignments of the same set of biological sequences and allows to annotate and comment the comparison. This allows life science researchers to decide which alternative alignments to take into account as the bases of e.g. a phylogenetic study or numerous other tasks.

More information can be found at

Source code

This GitHub repository in a synchronized mirror of the master repository at bioinfweb. Feedback and pull requests are welcome.


If you want to submit a bug report or feature request, please use our public bug tracking system at (We do not manage issues on GitHub directly.)


If you have questions, feel free to ask one on our ResearchGate project page or contact


AlignmentComparator is distrubuted under GNU General Public License Version 3. See NOTICE.txt for further details.

This product includes dependencies developed by the Apache Software Foundation distributed under the terms of the Apache License Version 2.0.

Binary releases

Binary releases can be found at

About bioinfweb