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Right now the control element DOM IDs are hardcore in the archaeopteryx.js. I do not know how to change it within html widgets. It may be that the only way is to move the dom ID for the control elements into the archaeopteryx instantiation function at which point it could be passed was a parameter.

after providing the ability to add multiple htmlwidgets per page I was getting errors with the node visualizations. This is probably due to the way that nodes are drawn (d3.selectall() etc). Look into it and see if there is a reasonable workaround otherwise there may be a fundamental limit to the number of widgets we can add per page.

allow adding taxonomy to nodes

associate sequences with nodes. may need to alter the phyloJ object to accommodate DNAStringSets