Roci reconstructs ancestral gene orders of a phylogenetic tree. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates sets of gene orders for the inner nodes, represented by conserved intervals.

The underlying Labelling-Algorithm is introduced in [BER:BLA:CHA:CHA:2004] by Bergeron et al. The implementation, including the enhancement to non-binary trees and a possible extension of the search space by reducible intervals, is described in [WIT:2006].