Abstract

Sequence logos are a common way to visually represent amino acid frequencies and conserved sequence patterns of multiple sequence alignments (MSAs). MSA Class Logos is a free web server that enables users to browse and explore sequence logos of several sequence groups or classes simultaneously online, and to download amino acid frequencies for the entire MSA or the sequence classes. Amino acid frequencies can be downloaded in tabular or graphical form for further offline analysis. The core feature of MSA Class Logos is the user’s ability to group amino acid sequences into classes or subgroups, generate sequence logos for each class, and compare the clearly arranged logos online. Sequence logos for the entire MSA and user-defined classes are generated in separate tabs and can be explored conveniently in parallel. Class-specific sequence logos facilitate the identification of class-specific conserved residues unique in evolutionary distant or functionally differing protein groups. Results can be explored visually directly on the web page or downloaded as tables in CSV format. Additionally, segments of each sequence logo can be downloaded in SVG format. MSA Class Logos is primarily intended for investigators without programming and scripting skills to ease detailed sequence analysis. © The Author(s) 2025. Published by Oxford University Press.