by Michael Charleston and Ran Libeskind-Hadas
Cophylogenetic analysis seeks to explain the relationships between mutually evolving pairs of species such as hosts and parasites. In the last two decades, increasingly sophisticated computational methods have been developed for performing cophylogenetic analyses. In particular, event-based reconstruction methods attempt to find the best supported reconstructions of pairs of related trees using a set of events including cospeciation, duplication, transfer, and loss. This chapter formulates the cophylogeny reconstruction problem, describes the algorithmic techniques that have been developed for this problem, and compares and contrasts the software packages that implement these methods.