Improved maximum parsimony models for phylogenetic networks

Phylogenetic networks arewell suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological...

Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and...

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...

Rearrangement moves on rooted phylogenetic networks

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based...