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The presence of reticulate evolutionary events in phylogenies turnphylogenetic trees into phylogenetic networks. These events imply in particularthat there may exist multiple evolutionary paths from a non-extant species toan extant one, and this multiplicity makes the comparison of phylogeneticnetworks much more difficult than the comparison of phylogenetic trees. Infact, all attempts to define a sound distance measure on the class of allphylogenetic networks have failed so far. Thus, the only practical solutionshave been either the use of rough estimates of similarity (based on comparisonof the trees embedded in the networks), or narrowing the class of phylogeneticnetworks to a certain class where such a distance is known and can beefficiently computed. The first approach has the problem that one may identifytwo networks as equivalent, when they are not; the second one has the drawbackthat there may not exist algorithms to reconstruct such networks frombiological sequences.  We present in this paper a distance measure on the class of tree-sibling timeconsistent phylogenetic networks, which generalize tree-child time consistentphylogenetic networks, and thus also galled-trees. The practical interest ofthis distance measure is twofold: it can be computed in polynomial time bymeans of simple algorithms, and there also exist polynomial-time algorithms forreconstructing 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 computationof the distance presented in this paper.

A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks