Exploring the space of gene/species reconciliations with transfers

Abstract

Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events). While numerous methods have been proposed to infer them, little has been done to study the underlying reconciliation space. In this paper, we characterise the reconciliation space for two evolutionary models: the (Formula presented.) (duplication, loss and transfer) model and a variant of it—the no-(Formula presented.) model—which does not allow (Formula presented.) events (a transfer immediately followed by a loss). We provide formulae to compute the size of the corresponding spaces and define a set of transfor..