There's a GSOC student, Sebastian Wilzbach, working on a JS MSA viewer, mentored by Tatyana Goldberg. This is his blog, which has some links to demos and this is the code.
Hi, that would be myself :)
The component is still in an alpha stage (we are currently working on a way to display >15k sequences). Nevertheless I am happy to help you if you want to experiment with a nightly version.
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