VISA (VIsual Sequence Analysis) is a software package that displays global similarities within a set of related protein sequences. The program identifies amino acid patterns that are common to many members of the set of sequences and displays them as a series of histograms. Individual peaks on the display can be assigned a color and analogous peaks in the other sequences are then automatically marked in the same color. This can be repeated for each significant peak and leads to a display in which major matching segments of multiple amino acid sequences appear as dominant peaks of the histograms with matching colors. These peaks usually correspond to the conserved sequence motifs that are characteristic of particular proteins. An extensive set of software tools is included to help the localization, visualization and analysis of the global similarities displayed. VISA provides a graphic overview of the sequence similarity that can help to understand the architecture of the protein family and can be helpful while designing experiments to probe function.