LalnView is a graphical program for visualizing local alignments
between two sequences (protein or nucleic acids). Sequences are
represented by colored rectangles to give an overall picture of the
similarities between the two sequences. Blocks of similarity between
the two sequences are colored according to the degree of identity
between segments.

A suitable alignment tool for protein sequences is SIM at ExPASy:
https://web.expasy.org/sim/

SIM finds a user-defined number of best non-intersecting alignments
between two protein sequences or within a sequence. Once the alignment
is computed, you can view it using LalnView.

For details and citation:
Duret, L., Gasteiger, E. and Perriere, G. (1996) LalnView: a
graphical viewer for pairwise sequence alignments. Comput. Applic.
Biosci., 12, 507-510
