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NetCooperate

A package for determining host-microbe and microbe-microbe cooperative potential. NetCooperate specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score and Metabolic Complementarity Index, which provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses.

NetCmpt

A tool for calculating the competitive potential between pairs of bacterial species. The score describes the effective metabolic overlap (EMO) between two species, derived from analyzing the topology of the corresponding metabolic models. NetCmpt is based on the EMO algorithm, developed and validated in previous studies. It takes as input lists of species-specific enzymatic reactions (EC numbers) and generates a matrix of the potential competition scores between all pairwise combinations.