Phylogenetic Information (phylogeny.dat)

Information about the phylogeny (ancestry) of all species that arise during a run is recorded in the file phylogeny.dat. Each line of this file is of the format:

SpeciesID,ParentSpeciesID

where ParentSpeciesID (the immediate ancestor of SpeciesID) is set to 0 for the record of a species that was used to inoculate the system at the start of the run. The entire phylogeny of any species can therefore be reconstructed from the data in this file, right back to an ancestor used to inoculate the system at the start of the run; the Perl script phyl will print the full phylogenetic tree for a species passed in as an argument.