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metabolisHMM is a tool for exploring and visualizing the distributions and evolutionary histories of specific metabolic markers. Annotating through Hidden Markov Model (HMM) based approaches is becoming increasingly popular over using BLAST-based methods. However, tools to reproducibly explore and visualize the distribution of these markers through constructing a phylogeny or summarizing a presence/absence matrix are lacking. This tool is a reproducible tool to search for, describe the results, and visualize any metabolic marker with an HMM profile. This wiki describes installing the required dependencies, how to use each workflow, and examples.