phylotree.js is a JavaScript library for phylogenetic tree visualization and analysis, designed for web-based applications. It provides robust parsing of multiple tree formats (Newick, PhyloXML, NEXUS, NEXML, BEAST), interactive SVG rendering via D3, and a suite of analytical utilities including metrics (Sackin's index, pairwise distances, root-to-tip regression), clustering algorithms (Cluster Picker, PhyloPart), and tree construction (neighbor joining). The library is modular, with separate modules for formats, rendering, metrics, and clustering, and includes CLI tools for common operations like rerooting, tagging, and validation. It is used in production at phylotree.hyphy.org and supports real-world phylogenetic workflows in molecular epidemiology and evolutionary biology. While the codebase demonstrates solid engineering with reusable patterns like an event emitter and a robust Newick parser, it shows signs of technical drift with legacy dependencies (underscore, lodash, moment) and some unused code.