Schema of a simple phylogenetic profiling pipeline. A) genes (dots) are grouped using a biologically relevant criterion (e.g. orthology) in a diverse set of genomes (rectangles). B) a matrix is constructed with rows corresponding to groups and columns corresponding to genomes. Each cell in the matrix is assigned a value of 1 (presence) or 0 (absence) of the group in the genome. C) this matrix is used as input to a phylogenetic profiling method that results in a list of potentially related gene groups. D) the output can then be used to build a functional network that may well lead to or give support to further biological findings.