 GRAPHLN is a graphical phylogenetic analysis tool designed to produce high quality, compact visualizations of microbial genomes and metagenomes. It can be used to generate phylogenetic trees spanning up to thousands of taxa, as well as annotate these trees with metadata such as microbial community abundance and microbial physiological or environmental characteristics. GRAPHLN is available both as a local command line tool and via an online Galaxy web application, making it easy to integrate into existing bioinformatics workflows. Examples of its use include taxonomic and phylogenetic visualization of microbial communities, metabolic function analysis, and biomarker discovery. This article was authored by Francesco Asnicar, George Weingart, Timothy L. Tickel, and others.