Figure 3

Schematic of bioinformatics fluidity pipeline. (A) Genomes are annotated automatically to minimize curation bias [39]; (B) For a given pair of genomes, all genes are compared using an all vs. all protein alignment; (C) Shared genes are identified based on whether alignment identity and coverage exceed i and c respectively; (D) Gene families are calculated based on a maximal clustering rule; (E) The number of shared genes is found for each pair of genomes, G _i and G _j , from which the number of unique genes can be calculated. Refer to the Methods for complete details of the pipeline and Additional file 1, Table S1 for a complete list of genomes analyzed.