A first step towards computing all hybridization networks for two rooted binary phylogenetic trees

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard approach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this paper, we make a first step towards approaching this goal by presenting the first algorithm---called allMAAFs---that calculates all maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on the same set of taxa.

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