Abstract
In the last decade, we witnessed the ascent of reconciliations as an important tool to model and study the evolution of gene families. Reconciliations model discordance between gene trees and species trees caused by gene-level processes: duplications, losses and transfers of genes, Incomplete Lineage Sorting among others can be combined to generate a panoply of different models. In this review article, we give an overview of this vast topic by skimming over the different models and methods that have been proposed, and presenting some of their applications in phylogenomics. We also present the pros and cons of these methods and give some directions for future research that we are convinced will enhance their efficiency and use.