  Understanding the dynamics of genome rearrangements is a major issue of
phylogenetics. Phylogenetics is the study of species evolution. A major goal of
the field is to establish evolutionary relationships within groups of species,
in order to infer the topology of an evolutionary tree formed by this group and
common ancestors to some of these species. In this context, having means to
evaluate relative evolutionary distances between species, or to infer common
ancestor genomes to a group of species would be of great help. This work, in
the vein of other studies from the past, aims at designing such means, here in
the particular case where genomes present multiple occurrencies of genes, which
makes things more complex. Several hypotheses accounting for the presence of
duplications were considered. Distances formulae as well as scenario computing
algorithms were established, along with their complexity proofs.
