For my work on the alignment of coiled-coil proteins, I needed an alignment viewer that could highlight coiled-coil domains, since they contain less phylogenetic signal than other parts of the protein. Adding this to JalView seemed very complicated, and not possible at all in other web-based viewers like MView. I therefore created amview (for "annotated multiple alignment viewer"), which looks like this in practice:
Shown is the MSA for spd-5 (and here is the entry in my coiled-coil orthologs database). Amino acids are colored according the ClustalW rules, coiled-coil residues are in a lighter color (and the "a" register of the heptad repeat is underlined). Below, two interaction domains are shown. At the very bottom, a small chart shows the degree of conservation across the whole alignment, which can be used to quickly scroll to the conserved regions. The cog on top hides two options: you can hide columns with too many gaps, and proteins that seem to be fragments.