GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms This suite of programs implements the approach to phylogeny reconstruction from gene orders described in the paper Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M., ``A detailed study of breakpoint analysis,'' Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001). In its current state, "grappa" allows one to explore either the space of all possible trees on n labelled leaves or the space of all such trees that obey (are refinements of) a particular constraint tree. "invdist" takes the first two genomes in the input file and returns their inversion distance. "distmat" prints the inversion and breakpoint distance matrices.