Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem

Benjamin Drinkwater, Michael A Charleston
2014 BMC Bioinformatics  
Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heavily on heuristics to solve all but the most trivial cases. One notable approach utilises a metaheuristic to search only a subset of the exponential number of fixed node orderings possible for the phylogenetic histories in question. This is of particular interest as it is the only known
more » ... istic that guarantees biologically feasible solutions. This has enabled research to focus on larger coevolutionary systems, such as coevolutionary associations between figs and their pollinator wasps, including over 200 taxa. Although able to converge on solutions for problem instances of this size, a reduction from the current cubic running time is required to handle larger systems, such as Wolbachia and their insect hosts.
doi:10.1186/1471-2105-15-s16-s14 pmid:25521705 pmcid:PMC4290644 fatcat:54zgfs5fs5bszhhmky26xiy2fe