Figure 2
From: A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
Illustration of the clustering method. The tree shown on the left side of the figure indicates the evolutionary relationships among several hypothetical organisms, four from Clade A, two from Clade B, and one that is an outgroup. The right side of the figure illustrates a protein distance graph with circles representing proteins colored to conform to each organism, with the spatial distance of the circles proportional to their sequence distance. The cluster is created by identifying a pair of sequences (a seed) that is the shortest distance from any Clade A protein to any Clade B protein. The cluster is then grown by adding all proteins that have a shorter distance than the seed until no additions can be made. The blue cloud represents one such cluster. See text for more details.