tax2tree assists in decorating an existing taxonomy onto a phylogenetic tree with overlapping tip names.
An example test tree and input consensus set can be found in tests/data. Once tax2tree is installed and paths are setup appropriately (see INSTALL), you can run the following to reproduce the output seen in Figure 1 in McDonald et al. 2011.
$ t2t decorate -t tests/data/test_consistency.ntree -m tests/data/test_consistency.cons -o test_output
Daniel McDonald (email@example.com)