I came across a nice program by Heroen Verbruggen called TreeGradients.
“TreeGradients is a tree drawing program. The tree drawing options are fairly basic but the program has the ability to plot several types of continuous variables at the nodes in colors and use linear color gradients to fill the branches between nodes. The output format is SVG (scalable vector graphics), which can be imported in most vectorial drawing software.”
It looks like Heroen is particularly interested in plotting continuous variables across trees. The part that immediately interested me was the ability to colour internal nodes by bootstrap (or Bayesian) support. In the example on the website poor support is given by pale greys along a gradient to strong support as black. When dealing with very large trees this is a nice visual trick to focus the mind on areas that are well supported and away from poorly supported areas (by making these less visible). Colours and presence of numeric bootstrap values can be adjusted to taste. The program is actually a pair of perl scripts distributed under an open-source GNU General Public Licence. I want to congratulate the author for making these open-source.
I haven’t actually tried it out yet but thought I’d flag it up now rather than my usual habit of waiting and waiting until I could review it properly (and my backlog is running at about 6 months now).