Sequences loaded in the viewer may be aligned by using a web-based alignment service that operates via Web Services interface. Therefore, in order for this function to operate, the client system must be online. Using the Alignment menu, it is possible to select the specific alignment algorithm, change parameters and save raw outoput of the alignment program once it has finished. While alignment is being performed, a red "Aligning..." text appears in the lower left corner of the sequence viewer.

Once the sequences are aligned, it is possible to evaluate distribution of side chains at any position within the alignment. The distribution is visualized as a bar graph with separate bars for each amino acid and its height proportional to the content of the corresponding amino acid. Data can be exported as graphics or CSV file, which can be convenient for large alignments.

Motif search scans loaded sequences for specified residue patterns and highlights hits. Any residue is denoted by an "X" in the query motif sequence.