Arborvisio

Arborvisio is the name of the result of my Bachelor thesis in Computer Science. I performed the thesis together with Robin Rosengren. Looking at the program you wouldn't guess I'm an interaction designer, but the focus this time around was a bit different.

The program is used to display phylogenetic trees which can be used to study relation between different species, proteins and so on. The application’s main use is intended to be together with ClustalW, for analyzing and displaying multiple sequence alignments of proteins and other biological groups. The output format of ClustalW is the Newick format, which basically looks like this (with some line breaks and indentation to make the tree structure more clear):

(
  Bovine:0.69395,(
    Gibbon:0.36079,(
      Orangutan:0.33636,(
        Gorilla:0.17147,(
          Chimp:0.19268,Human:0.11927
        ):0.08386
      ):0.06124
    ):0.15057
  ):0.54939,Mouse:1.21460
);


This particular tree would look like this when drawn in Arborvisio:

As can bee seen the application can draw three different types of trees, a radial tree, a cladogram and a phylogram. The application also allows the user to edit the presentation of the tree, but not the tree itself. An example of a customized radial tree can be seen below.

The application was developed i Java and licensed under GNU but is free for any and all non-profit fiddling. If you want to know more about the project you're also very welcome to read the project report. All these things can be found on the project site. The site is dated and contains documents originally meant for the project supervisor at school, but the code and report can be downloaded there (under download and documentation respectively) while the rest can be ignored.