Introduction to itep

With the rapidly decreasing cost of genome sequencing, most sequencing projects now involve the generation of many related sequences. ITEP is a collection of tools that automatically generates and organizes comparative genomics data and provides command line and programmatic interfaces for using this data to inform evolutionary studies. Capabilities of ITEP include:

• de novo protein family prediction by clustering,
• ortholog detection,
• analysis of functional domains,
• identification of core and variable genes and gene regions,
• analysis of gene gain and loss patterns according to the protein family predictions,
• sequence alignments, alignment curation and tree building,
• curation of annotations and gene calls,
• integration of cross-genome analysis and metabolic networks for study of metabolic network evolution

If this sounds useful, we recommend taking a look at the rest of the documentation in this wiki for details on how to set up the database and run the analysis you are interested in.