Figure 1

Overview of the ITEP toolkit. The ITEP toolkit is organized so that analyses can be performed in a three-step process. Step 1: The ITEP toolkit takes three inputs: Genbank files of genomes; user-defined groupings of input organisms in which to identify protein families; and clustering parameters that define the details of the clustering method used to identify the families. Step 2: The user calls provided setup scripts to build a SQLite database containing pre-computed data such as homology and clustering results. Step 3: After building the database, a user can use the provided interfaces to the database to identify core and variable genes, build protein and organism phylogenies, curate amd visualize protein families, or build draft metabolic reconstructions from a reference network. To accomplish ITEP interfaces with the SQLite database and many previously existing bioinformatics and programming packages [28–37].