tREeBOOT is a freely available command-line program written in Java by programming guru Stephen Smith that implements several methods for assessing phylogenetic uncertainty in supertrees, which were described in our recent paper, including:

• Bootstrap- or posterior probability-weighted MRP
• Source-tree bootstrapping
• Hierarchical bootstrapping

tREeBOOT enables source-tree bootstrapping and hierarchical bootstrapping based either on bootstrap profiles or posterior probability densities of source trees to estimate bootstrap proportions or posterior probabilities of nodes in the supertree, respectively.

tREeBOOT allows interpolation of the above algorithms with MRP, MinCut, and modified MinCut supertree estimation algorithms.

Requirements: tREeBOOT is a cross-platform application that requires installation of the Java Runtime Environment and works in conjunction with PAUP* and Rod Page's supertree program.