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Bioinformatics and Computational Biology


Network of 2,307 Proteobacterial bacteria.  The image shows the relationships of the different classes of bacteria within the phylum Proteobacteria.
Network of 2,307 Proteobacterial bacteria. Please see the Clusters page for a more complete description.
Network of 360 bacteria from all phyla available at NCBI.  This network shows the relationship of the different  bacteria considered.
A network of organisms assembled using homologous clusters obtained from the proteomes deduced from 360 complete bacterial genomes and retaining only the top 20% of the links between organisms (shared protein sequences). Phyla are assigned arbitrary colors. Nodes/Organisms are labeled using the first four letters of their particular phylum followed by their order. The network is created from all proteins shared by non-singleton (two or more sequences from different organisms) clusters. Therefore, it reflects the relationships between organisms both vertically and horizontally. In the network, organisms belonging to the same phylum often group together, e.g., Chloroflexi (seafoam green), Actinobacteria (red), Bacteroidetes/Chlorobi (light blue), and Cyanobacteria (light purple). The central section of the network has many organisms that are strongly linked to each other indicating that they share many homologous protein sequences. The Firmicutes (yellow) have a grouping that extends from the middle of the network, but are also distributed throughout this section. The nodes with larger circles indicate organisms isolated from their respective phyla; as discussed in the text, these organisms have numerous horizontally-transferred genes.