The way communities are assembled is an old ecological question currently experiencing renewed interest thanks to the recent advances in molecular biology and phylogenetics. The generality of these new methods has allowed us to understand the structure of communities of organisms from different kingdoms and at different scales. Concomitant with this growing interest, new methods, metrics, terms, and software have appeared that independently solve similar questions, but with different approaches. Here we provide a unifying framework on methods for community structure based on the relationships between four key concepts: phylogeny, phenotype, environment, and co-occurrence. The different approaches are based on different community representations of traits, the phylogenetic relationships of species in the community, or species occurrence along the environmental gradients. We finally provide insights on future directions of this emerging discipline.