TopiaryExplorer supports visualization of very large trees while providing convenient interfaces for decorating the tree with taxonomic information, automatically coloring branches based on data about environments where they are observed, selecting subtrees for independent analysis, interactive expanding and collapsing of clades, and many other features. TopiaryExplorer supports database connectivity, allowing investigators to obtain, combine, edit, search and save metadata from multiple studies. Multiple tree layouts such as rectangular or polar views are available and results can be exported as publication quality PDF images. Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, and Rob Knight; Bioinformatics, 2011; doi:10.1093/bioinformatics/btr517.