dave's blog of art and programming » bioinformatics http://www.pawfal.org/dave/blog missing acceptable use policy Fri, 10 Feb 2012 18:20:40 +0000 http://wordpress.org/?v=2.9.2 en hourly 1 Hapstar in Molecular Ecology Resources http://www.pawfal.org/dave/blog/2010/08/hapstar-in-molecular-ecology-resources/ http://www.pawfal.org/dave/blog/2010/08/hapstar-in-molecular-ecology-resources/#comments Mon, 23 Aug 2010 06:49:56 +0000 dave http://www.pawfal.org/dave/blog/?p=1428 Our hapstar paper has been published (actually a few weeks back):

Teacher AGF. Griffiths DJ (2010) HapStar: automated haplotype network layout and visualization. Molecular Ecology Resources

There is a preprint version available on the foam site.

]]> http://www.pawfal.org/dave/blog/2010/08/hapstar-in-molecular-ecology-resources/feed/ 0 Hapstar 0.5 http://www.pawfal.org/dave/blog/2010/01/hapstar-05/ http://www.pawfal.org/dave/blog/2010/01/hapstar-05/#comments Wed, 13 Jan 2010 14:56:40 +0000 dave http://www.pawfal.org/dave/blog/?p=971 Hapstar is released, and now has it's own website. Here's a screenshot of an example haplotype network of human and neanderthal DNA sequences.

]]> http://www.pawfal.org/dave/blog/2010/01/hapstar-05/feed/ 0 HapStar http://www.pawfal.org/dave/blog/2010/01/hapstar/ http://www.pawfal.org/dave/blog/2010/01/hapstar/#comments Fri, 01 Jan 2010 18:16:56 +0000 dave http://www.pawfal.org/dave/blog/?p=952 Hapstar is the new name for my little bioinformatics project, visualising population structure from differences between genetic sequences. The last few days I've done a lot of work on the GUI, allowing you to drag nodes around by hand, zoom in and out and navigate the graph. Also quite a bit of graph theory, validating the input graphs by detecting if they are a single connected component - or contain isolated graphs. It's already been used to produce figures for an upcoming publication, so hopefully I can show some real examples soon.

]]> http://www.pawfal.org/dave/blog/2010/01/hapstar/feed/ 0 Hapnet http://www.pawfal.org/dave/blog/2009/11/hapnet/ http://www.pawfal.org/dave/blog/2009/11/hapnet/#comments Wed, 11 Nov 2009 12:48:39 +0000 dave http://www.pawfal.org/dave/blog/?p=867 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.

]]> http://www.pawfal.org/dave/blog/2009/11/hapnet/feed/ 0