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TreeRot.v2b

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.

New Features:
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.

References cited

Complete documentation (pdf format)

Download program (MacBinary)    Download program (BinHex)

Suggested citation: Sorenson, M.D. 1999. TreeRot, version 2. Boston University, Boston, MA.