Orthology Inference: Methods, Benchmarking and Applications

PhD Thesis of Adrian Altenhoff on the topic of Orthology Inference. ETH Thesis Nr. 20636 accepted on the recommendation of Prof. Dr. Gaston H. Gonnet, Prof. Dr. Paul Thomas, Prof. Dr. Marc Robinson-Rechavi and Dr. Christophe Dessimoz. Orthologs are genes that started diverging through a speciation event; they are "the same genes in different species." Detecting the orthologs is an important prerequisite for many comparative genomics studies including species evolution and protein function prediction. This thesis revolves around problems to computationally infer orthologs: In the first part, I present a novel method to infer hierarchical orthologous groups followed by a contribution on how to benchmark orthology predictions based on real biological data. The second part of this thesis consists of different applications of orthology.