Mean values of gene duplication and loss cost functions

Abstract

Reconciliation based cost functions play crucial role in comparing gene family trees with their species tree. To provide a better understanding of tree reconciliation we derive mean formulas for gene duplication, gene loss and gene duplication-loss cost functions, for a fixed species tree under the uniform model of gene trees. We then analyse the time complexity and study mathematical properties of these formulas. Finally, we provide several computational experiments on empirical datasets for the duplication, duplication-loss and deep coalescence means under the uniform model.