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:
#nexus begin host; tree host=(a,(b,c)); endblock; begin parasite; tree parasite = ((I,II),III); endblock; begin distribution; range I : a, II : b, III : c; endblock;
Each file must contain HOST, PARASITE, and DISTRIBUTION blocks in that order.