  Orthology is a central concept in evolutionary and comparative genomics, used
to relate corresponding genes in different species. In particular, orthologs
are needed to infer species trees. In this chapter, we introduce the
fundamental concepts of orthology relationships and orthologous groups,
including some non-trivial (and thus commonly misunderstood) implications.
Next, we review some of the main methods and resources used to identify
orthologs. The final part of the chapter discusses the impact of orthology
methods on species phylogeny inference, drawing lessons from several recent
comparative studies.
