CTree is for viewing, analyzing and editing phylogenetic trees. There is a particular emphasis on the analysis of clusters within such trees. Clusters are stored as individual data structures from which statistical data can be easily extracted. Edit phylogenetic trees fats and easy.

Clusters can either be populated manually or alternatively via a novel heuristic algorithm that can automatically identify clusters on a tree (if they exist). The former is useful when previously published clusters are available while the latter is of use when control clusters across many random trees are required or when there are no previously published clusters.

Standard features include:
1. Ability to load multiple trees from a single file.
2. Re-rooting the tree.
3. Obtaining information such as pairwise distances between strains.
4. Swapping the order of sibling strains.
5. Manually removing strains (or groups of strains) from the tree.
6. Removing strains randomly from the tree.
7. An improved search interface that allows the user to color strains based on comma delimited search criteria.
8. Basic coloring of the tree.
9. Displaying various attributes on the tree such as strain labels, bootstrap values and evolutionary distances.
10. Allowing the user to obtain lists of strains within a user specified proximity to each other.
11. Allowing the user to define the distance covered by the scale bar associated with the tree.
12. Trees can be saved as publishable pdf format (using the iText library), newick format or java binary format (edits can be reloaded at a later date).
13. CTree deals well with large trees.

Requirements:
* Java

The license of this software is Freeware, you can free download and free use this graphing software.