Finding a most parsimonious or likely tree in a network with respect to an alignment

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant phylogenetic signals that were not present in the input. Here we show that, given a multiple alignment A for a set...

On computing the maximum parsimony score of a phylogenetic network

Phylogenetic networks are used to display the relationship among different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as maximum parsimony need to be modified in order to be applicable to networks. In this paper, we...

Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets...