ParaPhylo

ParaPhylo Overview

ParaPhylo is a tool for reconstructing phylogenetic species trees based on information about paralogous genes. It relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem.
Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements.

ParaPhylo relies on the IBM ILOG CPLEX Optimizer 12.6. for which an academic license can be obtained for free.