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).
EvoPhylo 
along these lines do you have a tree drawing software recommendation for linux. I used treeview in windows but it acts sort of funny on ubuntu. I dont need anything advanced, just something that can draw rooted or unrooted trees, and hopefully export in svg format. What would you suggest?
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This page lists a lot of tree editors, not absolutely up to date thoughhttp://www.treedyn.org/Tree_editors.htmlThis list is a great argument for open source software! How many times has the wheel been reinvented here?My favourites, hmm, I keep changing my mind. The page above is from the program treedyn, but it may be a bit unnecessarily complex for you from what you say. Here are three in no particular order that I think will be good for you to try-(1) I like Dendroscope for many reasons, it has a Linux version and does export svg.(2) I also like NJplot, simple reliable, nice basic features. Works. It has a linux version. I just noticed last week though that the export as graphic option has changed. Not sure how the Linux version behaves here. Doubt it supports svg though, shame.http://pbil.univ-lyon1.fr/software/njplot.html(3) FigTree is another favourite of mine. Good features. It has a java version to run on Linux, and allows export in lots of graphics formats including svg.http://tree.bio.ed.ac.uk/software/figtree/
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Thanks for the post – I like these graphical methods for showing tree details. Here is a recent discussion about doing this sort of thing in R:http://treethinkers.blogspot.com/2008/07/r-tip-indicating-tree-support.htmlI haven’t tried either method yet, so I can’t compare and contrast.
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Thanks Karen, you know all the time I was writing this I was thinking that I had seen something similar very recently! It was on the excellent Dechronization blog. Thanks for the heads up
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