GMWI2 (Gut Microbiome Wellness Index 2) is a robust and biologically interpretable predictor of health status based on gut microbiome taxonomic profiles. On a stool metagenome sample, this command-line tool performs four major steps: (1) Quality control; (2) Taxonomic profiling using MetaPhlAn3 (v3.0.13) with the mpa_v30_CHOCOPhlAn_201901 marker database; (3) Transformation of taxonomic relative abundances into a binary presence/absence profile; (4) Computation of the GMWI2 score using a Lasso-penalized logistic regression model trained on a meta-dataset of 8,069 health status labeled stool shotgun metagenomes.