A suite of tools for visualising sequence alignments.

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.
It has an extensive set of user-configurable modes to color residues
by conservation or by residue type, and some basic alignment editing
capabilities.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences. Every residue in one sequence is compared to every
residue in the other, with one sequence plotted on the x-axis and
the other on the y-axis.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/