Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications and annotations (i.e. protein domains). Here, we present the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.;MSABrowser is released as open-source and web-based software under MIT License. The visualizer, documentation, all source codes and examples are available at https://thekaplanlab.github.io/ and GitHub repository https://github.com/thekaplanlab/msabrowser.;Supplementary data are available at Bioinformatics Advances online.