Copyright (c) 2007 Michael D. Sorenson & Eric A. Franzosa
Department of Biology, Boston University, Boston, MA 02215

Description: TreeRot 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.v3 has been recoded in Perl and should now run on any operating system!

2.) TreeRot.v3 provides added functionality in the context of partitioned analyses (see Lambkin et al. 2002).

3). TreeRot.v3 outputs decay indices embedded in a NEXUS format tree for easy viewing in FigTree.

4.) TreeRot.v2 includes an option to generate the commands needed to calculate "partitioned" Bremer support (Baker & DeSalle 1997, Baker et al. 1998).

5.) TreeRot.v2 parses the PAUP log file and automatically calculates decay indices.

Bug Fix 5/28/08: Minor bug fix affecting parsing of PAUP output files in which maxtrees limit was reached. Please download new version if you obtained the program prior to 5/28/2008.

Bug Fix 5/7/08: Minor bug fix affecting parsing of some PAUP output files.

Bug Fixes 3/12/08: Various fixes to minor and not so minor problems in the new code. Please download new version and re-check analyses for accuracy if you obtained the program prior to 3/12/2008.

Bug Fix 9/17/07: TreeRot.v3 made more forgiving of variation in the format of input tree file.

References cited

Documentation (pdf format)

Download program (.sit)   

Download program (.tgz)

Download program (.zip)

TreeRot.v2 (for classic Macs only)

Suggested citation: Sorenson, M.D. & E.A. Franzosa 2007. TreeRot, version 3. Boston University, Boston, MA.