The cladistics package in PAST is fully operational, but is lacking comprehensive functionality. For example, there is no character reconstruction (plotting of steps on the cladogram). The use of PAST in parsimony analysis should probably be limited to entry-level education and preliminary investigations. The parsimony algorithms used in PAST are from Kitching et al. (1998).

Character states are coded using integers in the range 0 to 255. The first taxon is treated as the outgroup and will be placed at the root of the tree. Missing values are coded with a question mark. There are four algorithms available for finding short trees: branch-and-bound (finds all shortest trees), exhaustive (finds all shortest trees, and allows the plotting of tree-length distribution), heuristic nearest neighbor interchange (NNI) and heuristic subtree pruning and regrafting (SPR). Three different optimality criteria are available: Wagner (reversible and ordered characters), Fitch (reversible and unordered characters), and Dollo (irreversible and ordered). Bootstrapping can be performed with a given number of replicates.

All shortest (most parsimonious) trees can be viewed. If bootstrapping has been performed, a bootstrap value is given at the root of the subtree specifying each group.

The consensus tree of all shortest (most parsimonious) trees can also be viewed. Two consensus rules are implemented: strict (groups must be supported by all trees) and majority (groups must be supported by more than 50% of the trees). PAST can read and export files in the NEXUS format, making it compatible with packages such as PAUP and MacClade.