MSA Class Logos is a free webserver allowing the user to group amino acid sequences into classes and to generate sequence logos for each class and the entire multiple sequence alignment. The input files are a multiple sequence alignment in FASTA format and a file that specifies the class each sequence belongs to in CSV format. After file upload, one reference sequence needs to be selected. This sequence will be displayed separately for comparison. This can be any sequence from the multiple sequence alignment and is just for convenience in case it is interesting to compare a certain sequence to the sequence logos of each class. If this is not of importance, any sequence can be selected since it does not affect the generation of the logos and therefore the results displayed. There are two tabs with different results available. The first one shows the complete multiple sequence alignment with all sequences sorted according to the classes defined by the user and a sequence logos considering all sequences. The second one shows separated sequence logos for each defined class which allows the identification of positions that are conserved only in a subset of sequences. In other words, the second view (tab) allows a more detailed analysis of a multiple sequence alignment that permits the identification of class specific conserved residues in evolutionary and/or functionally variable protein groups. Results can be reviewed visually directly on the web page or downloaded as tables in CSV format. Additionally, sections of each sequence logo can be downloaded in SVG and used for the generation of figures for publications or presentations, for example. This step-by-step description of how to use MSA Class Logos uses the example files available on the web server.