TopiaryExplorer is now being developed on GitHub
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).
TopiaryExplorer v1.0 Release Notes
New Features
- Select color for unmapped nodes
- Select no count color
- Generate figures over metadata category
- By-value coloring for numerics
- Mouse scrolling works in tree view
- Added distance from parent collapsing
- Metadata corresponding to pruned nodes is removed from tables when project is saved
- Export list of node names
- Branch width by abundance
Changes
- Refactored interpolate so it takes less time
- Interpolate is now Apply Colors and colors are only changed when that button is clicked
- TreeToolbar interface standardized
- Updated user guide
Bug Fixes
- Fixed radial view rendering bug
- Radial wedge labeling fixes
- Ladderize fix
- Export radial, polar image labeling fixes
- Bug fix for columns containing string and numeric values crash
- Allow double type in otu tables
- Save tree as newick string fix
- Color by new column
- Fixed issue where full consensus lineage isn't available in the tree right click menu
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
