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metabolisHMM is a tool for visualizing the distributions and evolutionary histories of specific metabolic markers. Functional annotation 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 composed of reproducible workflows to search and and visualize any metabolic marker with an HMM profile among any set of sequenced genomes. This wiki describes installing the required dependencies, how to use each workflow, and examples.