Abstract
Summary Phylogenetic inference is the process of searching and reconstructing the best phylogenetic tree that explains the evolution of species from a given data set. It is considered as an NP‐hard problem due to the computational complexity required to find the optimal phylogenetic trees in the space of all the possible topologies. We have developed MO‐Phylogenetics, a software tool to infer phylogenetic trees optimizing two reconstruction criteria simultaneously, integrating a framework for multi‐objective optimization with two phylogenetic software packages. As a result, researchers in life sciences have at their disposal a high‐performance tool including a number of multi‐objective metaheuristics that can be applied to phylogenetic inference using the maximum parsimony and maximum likelihood as objectives to be optimized at the same time.
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