The FigTree software is used a lot in my group for plotting phylogenetic trees, and makes lovely pictures.
Running FigTree on the Sanger farm: [of interest to Sanger users only]
% ssh -Y farm3-login
% bsub -o o -e e -R "select[mem>1000] rusage[mem=1000]" -M1000 "/software/bin/java -Xmx1G -jar ~bh4/apps/FigTree_v1.4.2/lib/figtree.jar"
(This has to be bsubbed, for some reason it won't run on the head node)
Once FigTree has opened, load the tree using File->Open.
Thanks to my colleague Bhavana Harsha for help with this.