A while back I talked about the software in the gibbon genome paper. I went through to try to pull out as much of the software as I could as sort of a catalog of a representative genome project. Of course, there was a lot in there. Some of it, though, consisted of unpublished code.
One of the figures I liked very much because it contained a lot of information quickly was this Figure 2 from the main paper, with the Oxford plots for comparison, and then the view of the phylogenetic tree. I mused about whether this was available somewhere, and I contacted the team to find out. Javier Herrero has been really terrific about answering my questions and getting back to me with more details. The plot code was an internal script, and the tree layout wasn’t a special tool, but just a graphical arrangement done by hand later.
So knowing my interest in this software, Javier let me know the other day that he’s put that code for the plots on Github. You can access it yourself there. Note–it requires eHive and Kent libraries. And this makes the dot plots, but you still would have to lay out the tree by hand.
But now you can plot these types of comparisons if you want to try it out.
Oxford plots: https://github.com/jherrero/oxford-plots
Carbone L., R. Alan Harris, Sante Gnerre, Krishna R. Veeramah, Belen Lorente-Galdos, John Huddleston, Thomas J. Meyer, Javier Herrero, Christian Roos, Bronwen Aken & Fabio Anaclerio & al. (2014). Gibbon genome and the fast karyotype evolution of small apes, Nature, 513 (7517) 195-201. DOI: http://dx.doi.org/10.1038/nature13679