Indirect identification of horizontal gene transfer

Abstract Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence two species in which reside. This situation defines edge set a graph, later-divergence-time (LDT) whose vertices correspond colored by their species. We investigate these graphs setting relaxed scenarios, i.e., evolutionary scenarios encompass all commonly used variants duplication-transfer-loss literature. characterize LDT as subclass properly vertex-colored cographs, and provide polynomial-time recognition algorithm well an construct scenario explains given LDT. An graph implies corresponding are separated at least one HGT event. The converse is not true, however. show complete xenology relation described rs-Fitch multipartite satisfying constraints vertex coloring. class also recognizable polynomial time. finally address question “how much information about events contained graphs” with help simulations wide range duplication, loss, events. In particular, we simple greedy editing scheme can be efficiently detect implicitly graphs.