Data file format

The data file format for TreeMap 2.0 is the same as for TreeMap 1.0.

TreeMap uses a variant of the NEXUS format to describe the host and parasite trees, the host-parasite associations, and the reconstructions. Extensions to the NEXUS format are currently being developed (David Maddison, pers. comm.) that will enable us to replace the current format with a more portable format. In the meantime, TreeMap has its own file format. Here is a simple example:


begin host;
     tree host=(a,(b,c));

begin parasite;
     tree parasite = ((I,II),III);

begin distribution;
          I : a,
         II : b,
        III : c;


Each file must contain HOST, PARASITE, and DISTRIBUTION blocks in that order.