Cite TopiaryExplorer with the following reference:

TopiaryExplorer: An application for connecting large phylogenetic trees to environmental metadata; Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, and Rob Knight (Bioinformatics 2011).

Current technologies for high-throughput sequencing provide an investigator with massive amounts of data that are most easily interpreted with use of appropriate graphical models. In microbial ecology studies, the use of a phylogenetic tree can provide powerful insight into the structure of microbial hierarchies.

Topiary Explorer is an innovative phylogenetic tree-viewing program written in Java that, unlike most phylogenetic tree-viewing software currently available, integrates the tree along with its related metadata. This tree-metadata relationship facilitates easy identification of interesting inferences by way of automated tree coloring.

Topiary Explorer handles tip-related metadata, such as OTU metadata, as well as more generalized group metadata by way of a tip to group table and group metadata, commonly in the form of sample metadata. In addition to automated tip coloring, tips can also be automatically labeled with related metadata. Principal coordinates analysis visualizations are available in the stand-alone, offline version of Topiary Explorer, and are also colored automatically based on supplied metadata.

Topiary Explorer acts as an analysis pipeline, keeping all phylogenetic tree related information in one place so that data analysis is more interactive and easier for the researcher.

You can download Topiary Explorer using SVN

1. svn co https://topiaryexplorer.svn.sourceforge.net/svnroot/ topiaryexplorer/trunk/main topiaryexplorer
2. cd topiaryexplorer
3. javaws topiaryexplorer.jnlp