Tuesday 3 June 2014

Using FigTree for plotting phylogenetic trees

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.

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