toytree is a mature Python library and CLI toolkit for phylogenetic analysis: parsing and writing Newick/NEXUS trees, manipulating tree topology, simulating random and coalescent trees, inferring trees with NJ/UPGMA/consensus/parsimony, computing tree distances, running phylogenetic comparative methods (PIC, PGLS/PGLM, discrete/continuous trait evolution), and drawing publication-quality SVG/HTML figures through toyplot. The codebase is organized as a modular set of subpackages (io, core, drawing, mod, pcm, rtree, infer, enum, distance, annotate, otol, network) with a consistent lazy-import API and a method-binding decorator pattern that attaches subpackage functions to ToyTree objects. A full command-line interface exposes many of these operations and uses a custom binary serialization transport for piping trees between subcommands. The repository also includes a large, versioned validation harness for penalized-pseudolikelihood molecular dating and trait simulators, giving it a hybrid research-data flavor underneath its primary application/library character.