Category Archives: genetics viz

Hapnet

A small bioinformatics project in progress:

Haplotype networks and Minimum Spanning Networks are commonly used for representing associations between sequences. HapNet is a tool for viewing both types of networks, using the output data generated from Arlequin. HapNet automatically formats the network in the optimal layout for easy visualisation, and publication-ready figures can be exported in several formats.

After calculating the minimum spanning trees of the networks, my initial reaction was to use graphviz for this, as it seems perfect for the job. However, I had a lot of trouble with the different length edges, and the need to represent distance with intermediate nodes which have to be on a straight path. As I’d already written force directed graph drawing for daisy it wasn’t too hard to adapt. Source code here, and the start of a proper webpage on the libarynth.

Accidental graph art

If I ran one of these new fangled ‘new media arts’ courses (or whatever they are called now) I’d force students to restrict themselves to only using graphviz for several months. These are some accidents which happened trying to visualise haplotype networks for some biology visualisation work I’m doing:

Alex Mclean has some more impressive graphviz drawings here. I’m actually having to abandon graphviz as it wont cope with different length edges very well. I expect this will come back to bite me.