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Companion Applications

A number of PAUP* users have suggested that the following applications are useful companions to PAUP*. By no means is this list intended to be comprehensive. If you know of others please tell us about them.

If you are interested in phylogeny software in general, Joe Felsenstien maintains a website with descriptions and links to more than 100 phylogeny programs.

AutoDecay by Torsten Eriksson generates Decay Indices from a PAUP* treefile. AutoDecay will run on Macintosh, Windows or various Unix (Linux) versions and may be downloaded for free at

Executor by ARDI allows users to run the Macintosh 68k no FPU version of PAUP* 4.0 on PCs running Windows or Linux. A demo verison of Executor is available at

Freqpars by David Swofford analyses gene frequencies under the parsimony criterion. Swofford and Berlocher describe the method in Systematic Zoology 36: 293-325, 1987. The software is out-of-date and is not being support. A PC version, the FORTRAN 77 source code, and some documentation are available at

MacClade by Wayne Maddison and David Maddison ( is a computer program for phylogenetic analysis and provides an easy to use interface for editing data. MaClade will run on a Macintosh and is distributed by Sinauer Associates, Inc. A demonstration version of MaClade can be downloaded at the MaClade website

ModelTest by David Posada ( uses PAUP* to generate the likelihood scores for models of DNA evolution and then helps the user choose the model that best fits his/her data. ModelTest runs on a Macintosh, PC, or Sun and may be downloaded for free at

NDE (NEXUS Data Editor) by Rod Page ( is a program to create and edit NEXUS formatted files. NDE will run on Windows 95/98/NT and may be download for free at

RepMaker by Jim Wilgenbusch is a simple perl utility for automatically making multiple NEXUS files. Files can be used to distribute a single PAUP* bootstrap analysis over multiple machines using the scheduler Condor or the perl utility BsLauncher (included with RepMaker). Download RepMaker at

Se-Al by Andrew Rambaut ( creates multiple sequence alignments from nucleotide and amino acid sequences. Se-Al will run on a Macintosh and may be downloaded for free at

TreeEdit by Andrew Rambaut ( is an application for organising, viewing and manipulating sets of phylogenetic trees. It is intended as a tool for preparing sets of trees for use in phylogenetics packages such as PAUP. TreeEdit will run on a Power Macintosh and may be downloaded for free at

TreeView by Rod Page ( reads and writes NEXUS, PHYLIP, and Hennig86 tree files and can also save trees in graphic formats. TreeView will run on a Macintosh or PC and may be downloaded for free at


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