FeedUtiliGene has a modular structure, the software application consists of eight modules. Some of them are independent from the others while some of them expect results from other modules. The modules of digestion and nutrient partitioning (post-digestive models including the fitted growing pig model, the fatty acid model and the fitted broiler model) have many functions and the user can simulate different scenario by changing traits (input parameters) related to feed, animal or environment. Thus, it provides a tool to improve understanding on feed use mechanisms in pigs and poultry. Working with post-digestive models require to run the parameter estimation module in advance. The parameter estimation modules for pigs and chicken provide a tool to characterise the individuals in a herd or flock by the key parameters as defined in the post-digestive model. The perturbation module shows the steps of the statistical procedure to estimate the resistance and resilience of an animal based on their cumulative feed intake curve. The feed intake analysis procedure has proved its capacity to detect and quantify the response of animals to perturbations. These traits can be a potential source for genetic selection to breed animals for enhanced robustness. Stochastic module provides the individual variance of a herd, the descriptive statistics on and correlation between the 5 initial variables. It includes a procedure to demonstrate the reliability of the number of resampling to estimate the individual variation within a herd.