The Pathos analytical environment (http://compbio.mcs.anl.gov/pathos), and its cognate knowledge-base, PathoGene (http://compbio.mcs.anl.gov/pathogene) have been developed in the framework of the Microbial Informatics Core of the GLRCE to support infectious disease research. These resources allow researchers to (1) identify potential pathogenic factors (2) use metabolic reconstructions to predict essential genes in pathogenic organisms (3) explore pathogen-host interactions (e.g. cases of potential molecular mimicry, analysis of pathogen’s secretome). Pathos is an interactive integrated computational environment for genetic sequence analysis and reconstruction of metabolic and pathogenic pathways. It provides access to the results of precomputed genetic sequence analysis and automated metabolic reconstructions for over 170 publicly available genomes of pathogenic organisms. Pathos supports comparative analysis of sequence data and metabolic networks in the framework of taxonomic and physiological information. To facilitate identification and characterization of pathogenic factors, Pathos also allows interactive analysis of sequence data and metabolic networks by over 30 bioinformatics tools.