Figure 2

Illustration of ITEP’s capabilities for studying gene gain and loss patterns across a phylogeny. The node labels are the number of gene families (as computed by an MCL clustering of BLASTP results for both complete and draft genomes) that have at least one representative in each child of that node. Labels also contain a node identifier (N95) that can be used to look up the identities of all of the conserved families in tables outputted by the program. Examples of conserved families at node N95 are shown beneath the tree. The tree was generated from a concatenated alignment of ribosomal proteins uniquely identified in all of the genomes (17 families) with ITEP’s scripts, using FastTree [36] and a WAG model of evolution. Clusters were generated with the parameters: MCL clustering, inflation parameter of 2.0 (default for MCL), maxbit score, cutoff of 0.3. The tree was drawn with FigTree [43].