Have you thought about combining the dendrogram with a
Could ClusterPlot be combined with pcolor() to do this?
To be honest, I haven't thought about doing anything like this. While I'm using the Pycluster package to do my cluster analysis, I'm actually doing research in Physics Education, not genetics. As a result, I've never even seen diagrams like the one shown in the above link before. Looking at it, however, I imagine that with the judicious use of subplots, ClusterPlot could create the dendrograms in those images. Once direction control is added to ClusterPlot, that is.
At this point I have thought about only two further extensions to ClusterPlot. The first is the afore mentioned one: allowing control of the direction of the dendrogram. Once that's implemented, I'd consider the code to be out of the beta stage. The other extension would be a modification to the coordinates function so that the vertical coordinates of the dendrogram don't have to follow the Pycluster distances in the tree. Pycluster doesn't support having anything other than a distance measure in that slot. Now, while Pycluster does have 8 different distance measures, I can imagine cases where one would prefer to spread the tree by a dissimilarity measure or some other metric. This modification should be simple enough to make, so it'll probably be included in the next update (which might come before full release).
Finally, concerning the license discussion, I've posted version 0.6 which is released under the BSD-style license. Version 0.5, with its GPL license has been removed from the download site.
R. Padraic Springuel
Department of Physics and Astronomy
University of Maine
Office Hours: Wednesday 2-3pm