Rococo

Rococo reconstructs ancestral gene clusters. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates optimal sets of gene clusters for the inner nodes. The optimization criterion combines two properties: parsimony, i.e. the number of gains and losses of gene clusters has to be Minimal, and consistency, i.e. for each ancestral node, there must exist at least one potential gene order that contains all the reconstructed clusters.