Fluxer is a web application for the computation and interactive visualization of flux graphs from genome-scale metabolic models. Flux Balance Analysis is used to calculate the flux of the metabolic network, which can then be visualized with spanning trees, k-shortest paths, and complete graphs. More than 100 genome-scale metabolic networks are currently pre-loaded in the application and available for visualization. In addition, any user can upload their own SBML metabolic models for Fluxer to compute, analyze, and visualize their flux graphs. New models can be created by merging two or more models with mergem, which can also be used to visually compare multiple models. Generated graphs can be downloaded as high-quality images or GraphML and models as SBML.