  The presence of reticulate evolutionary events in phylogenies turn
phylogenetic trees into phylogenetic networks. These events imply in particular
that there may exist multiple evolutionary paths from a non-extant species to
an extant one, and this multiplicity makes the comparison of phylogenetic
networks much more difficult than the comparison of phylogenetic trees. In
fact, all attempts to define a sound distance measure on the class of all
phylogenetic networks have failed so far. Thus, the only practical solutions
have been either the use of rough estimates of similarity (based on comparison
of the trees embedded in the networks), or narrowing the class of phylogenetic
networks to a certain class where such a distance is known and can be
efficiently computed. The first approach has the problem that one may identify
two networks as equivalent, when they are not; the second one has the drawback
that there may not exist algorithms to reconstruct such networks from
biological sequences.
  We present in this paper a distance measure on the class of tree-sibling time
consistent phylogenetic networks, which generalize tree-child time consistent
phylogenetic networks, and thus also galled-trees. The practical interest of
this distance measure is twofold: it can be computed in polynomial time by
means of simple algorithms, and there also exist polynomial-time algorithms for
reconstructing networks of this class from DNA sequence data.
  The Perl package Bio::PhyloNetwork, included in the BioPerl bundle,
implements many algorithms on phylogenetic networks, including the computation
of the distance presented in this paper.

Populations and Evolution;Computational Engineering, Finance, and Science;Discrete Mathematics