Phylo-VISTA is an interactive tool for analyzing multiple DNA sequence alignments by vizualizing a similarity measure for DNA sequences for different species while considering their phylogenic relationships. Features include multiple-resolution visualization for examining an alignment and easy comparison of any subtree of sequence data within the complete alignment dataset.
Try the applet with this example.
This server runs PHYLO-VISTA v.2.2 (09/24/04).
Note that the MLAGAN multi alignment server uses PHYLO-VISTA for visualization.