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 http://www.bergianska.se/index_forskning_soft.html.
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 http://www.ardi.com/executor.php
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 The software is out-of-date and is not being support.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 http://paup.csit.fsu.edu/freqpars/.
MacClade by Wayne Maddison and David Maddison (email@example.com) 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 http://phylogeny.arizona.edu/macclade/macclade.html
ModelTest by David Posada (firstname.lastname@example.org) 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 http://bioag.byu.edu/zoology/crandall_lab/modeltest.htm.
NDE (NEXUS Data Editor) by Rod Page (email@example.com) 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 http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html.
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 http://paup.csit.fsu.edu/scripts/repmaker.tar.gz
Se-Al by Andrew Rambaut (firstname.lastname@example.org) creates multiple sequence alignments from nucleotide and amino acid sequences. Se-Al will run on a Macintosh and may be downloaded for free at http://tree.bio.ed.ac.uk/software/seal/
TreeEdit by Andrew Rambaut (email@example.com) 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 http://evolve.zoo.ox.ac.uk/software/TreeEdit/TreeEdit.html
TreeView by Rod Page (firstname.lastname@example.org) 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 http://taxonomy.zoology.gla.ac.uk/rod/treeview.html.