 The development of GRAPHLN, a computational tool, provides high-quality visualizations of microbial genomes and metagenomes with phylogenies spanning thousands of taxa, annotated with metadata ranging from microbial community abundances to physiology or host and environmental phenotypes. It is designed as an open-source command-driven tool that can be easily integrated into complex bioinformatics pipelines and executed locally or through an online Galaxy Web application. GRAPHLN's potential for modern microbial and community genomics is illustrated by several examples, including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery. This article was authored by Francesco Asnicar, George Weingart, Timothy L. Tickle, and others.