Description: TreeRot is a Macintosh program that aids in the determination of decay or Bremer support indices (Bremer 1988) by generating a command file for PAUP or PAUP* (Swofford 1993, 2002). The command file includes 1) a constraint statement for each node in a given shortest or strict consensus tree and 2) commands to search for trees inconsistent with each of these constraint statements in turn.
1.) TreeRot.v2 includes an option to generate the commands needed to calculate "partitioned" Bremer support (Baker & DeSalle 1997, Baker et al. 1998).
2.) TreeRot.v2 now parses the PAUP log file and automatically calculates decay indices.
Bug Fix 11/24/99: TreeRot.v2a fixes a bug in the second stage of the program (New Feature #2 above) that was a problem only when fractional character weights or stepmatrices with fractional weights were in use.
Bug Fix 7/28/00: TreeRot.v2b fixes a bug in the second stage of the program that was a problem only when tree lengths exceeded 32,000 steps.
Bug Fix 10/31/02: TreeRot.v2c fixes a bug in the second stage of the program that was a problem when multiple MP trees were found in partitioned Bremer analyses.
Complete documentation (pdf format)
Download program (MacBinary) Download program (BinHex)
Suggested citation: Sorenson, M.D. 1999. TreeRot, version 2. Boston University, Boston, MA.