Lpnet: Reconstructing Phylogenetic Networks from Distances Using Integer Linear Programming

We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We use integer linear programming to replace a heurisristic part of the agglomeration procedure based on local information by an exact global solution. This approach achieves an improved approximation of the input distance for the clear majority of experiments that we have run for simulated and real data. We release an implementation in R that can handle up to 94 taxa and usually needs about one minute on a standard computer for 80 taxa.