Example
newick -conf reference.newick -trees replicates.newick -output conftree.newickDescription
The newick command-line utility has tools for manipulating trees in Newick format.
The conf command calculates bootstrap confidence values by comparing a reference tree to a set of replicate trees. The output tree has confidence values stored as node labels.
The newick utility supports Felsenstein confidence, but not transfer expectation. If you want transfer bootstraps, you can use the RAxML support command.
