PARANA is an implementation of the method to perform parsimony based inference of ancestral biological networks. Given multiple extant networks and phylogenetic information relating extant nodes, PARANA finds a parsimonious set of ancestral interaction events (edge gains and losses) which explain the extant networks.
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R. Patro, E. Sefer, J. Malin, G. Marçais, S. Navlakha and C. Kingsford.
Parsimonious Reconstruction of Network Evolution.
Algorithms for Molecular Biology 7 (2012): 25