bremer.tcl is a Tcl script designed and implemented by M. Göker to compute Bremer and partioned Bremer support values in conjunction with PAUP*. It converts a MP strict consensus treefile to a batchfile for PAUP* including inverse constraint commands for each split of the consensus tree. After the PAUP* run, the script computes the support values from the resulting logfile. If the original consensus tree is provided, support values are inserted as internal egde labels.
In order to run the script, you need to install Tcl as well as tcllib. In order to run the batchfile, you will need PAUP*. After installing Tcl and tcllib, the script runs as a command-line application under Mac OS 10 and UNIX/Linux operating systems. Make sure that you have execution permissions (enter: "chmod 755 bremer.tcl"). In order to run the script under Windows, follow the general instructions for running Tcl scripts found at numerous locations in the WWW.
Make sure that you enter the heuristic search settings in your data file using PAUP*'s "defaults" command. If you want to compute partitioned Bremer support values, you need appropriate "charset" commands in the "assumptions" block. See the example files below for more details.
Some characters in taxon labels will conflict with the parsing of the consensus tree as exported from PAUP*. In case the taxon labels are not enclosed in single quotes, the script is expected to result. If the labels are enclosed in single quotes, whitespace and the characters []{}(),: must not occur within the labels.
If you use this script in a publication, please cite Göker et al. 2009.
As tutorial has been compiled for one of my phylogeny courses.
In case you have any questions regarding this script, send an e-mail to support [AT] goeker [DOT] org. Please include "bremer" somewhere in the subject.