bonsai is a freely available program written in Java that can run on Macintosh OSX, Windows, Linux, and Unix operating systems that implements several functions for grooming individual or posterior densities of phylogenetic trees, including:

• Pruning out burn-in samples of trees
• Thinning a posterior density of trees
• Filtering a posterior density for trees with a specific clade
• Grafting species to tree tips as terminal polytomies

bonsai originated as a simple 'helper' program for preparing input files for SymmeTREE analyses; for example, to perform taxon substitution (to accommodate incomplete species sampling), to manipulate posterior densities of trees (to accommodate phylogentic uncertainty), and to filter posterior densities for trees that contain a target clade (which may be of interest, e.g., as the locus of a diversification rate shift, or in the context of ancestral-state estimation).

Requirements: bonsai is a cross-platform application that requires installation of the Java Virtual Machine and works in conjunction with output from MrBayes.

bonsai is currently under development...very, very slow development.