Derek S. Sikes

Curator of Insects
Assistant Professor of Entomology
University of Alaska Museum
907 Yukon Drive
Fairbanks, AK 99775-6960

email: ffdss 'at'


A tool to implement Parsimony and Likelihood Ratchet searches using PAUP*


Derek S. Sikes and Paul O. Lewis 
Department of Ecology and Evolutionary Biology
University of Connecticut
Storrs, CT 06269

June, 2001

PAUPRat is a program to generate a text file that contains commands which, when read by PAUP* (with an open and executed data file), will implement the Parsimony Ratchet of Kevin Nixon; or, if modified, the Likelihood Ratchet of Rutger Vos (see below). The Ratchet is a search strategy that is surprisingly efficient at finding shortest trees for data sets too large for traditional heuristic search methods.


Download the manual ( 148 k pdf file)


Download the Macintosh [GUI command line] version (256 k)

Download the Windows [DOS command line] version (92 k)

Download the UNIX [terminal command line] version (168 k)

Download the Mac OS X UNIX [terminal command line] version (336 k)

source code:

NEW! Download the Linux / MacOS X source code and instructions for building (19k). [not covered in manual]

R. A. Vos has adapted the Ratchet idea to work in Maximum Likelihood analyses. He describes this procedure, which involves preparing a modified input file for PAUPRat, in: Vos, R. A. 2003. Accelerated likelihood surface exploration: The likelihood ratchet. Systematic Biology 52(3): 368-373. He has also created a website with information and a draft of the above paper in pdf form.


Legal stuff: PAUPRat is a beta freeware application without warranty or support. Use at your own risk.



Copyright 1999-2004 Derek S. Sikes and Paul O. Lewis