PaupUp: A free graphical frontend for Paup* DOS software

© 2005-2007 Frédéric Calendini & Jean-Francois Martin

Current version is


PauUP program is developped to provide a user-friendly interface to the phylogenetic program PAUP* on Windows operating systems. The DOS version of PAUP* is entirely command-line driven and does not provide any graphical interface. PaupUp partly resolves this issue, providing around 80% of the available commands (the most commonly used in our opinion) in a graphical environment comparable to the MAC OS version while the last 20% commands are still available through direct command-line input in a single integrated design. Further, graphical output of trees is allowed through Treeview integration as an external module and direct transparent implementation. Finally, the integration of Modeltest (most parameters available) is provided in a similar transparent design. We hope that PaupUp will help many people in their research and teaching activities as it proved useful for us in the last couple of months when testing the software. WARNING : PaupUp is not compatible with Windows version of PAUP* but this should not be an issue as both DOS and Windows versions of PAUP* are purchased together in the same package.

NEW : the new revised version includes the correction of bugs reported so far, in particular the issues related to tree sorting and commands being too long for DOS. Furthermore it also includes a link with modeltest that allows the user running a full modeltest run within the PaupUp interface. Of course and as usual Modeltest software is not provided with the package as we are not responsible for its distribution.

New 03.19.2007 : Release of PaupUp : correction of a bug in the distance settings menus.

Screenshot 1 - Screenshot 2

Overview - how to get started
The purpose of PaupUp is not to replace PAUP* DOS version but instead to provide an easier access to its main commands and parameters settings. It is therefore not a standalone software and PAUP* DOS version is still necessary.

Installation procedure

The installation is straightforward but requires that the Microsoft® .NET 2 Framework is installed on your computer. This is usually the case when Windows update are done regularly but it may be absent from older systems. The .NET framework 2 package is available for free here and should be installed prior to PaupUp installation. When first launched, PaupUp opens the preferences settings and asks you to enter the full path of PAUP.exe on your hard drive. It is a good idea to provide such information for Treeview and Modeltest packages at the same time as they both are very useful packages fully integrated in PaupUp. PaupUp needs to be restarted to take the provided paths into account. If the program still does not detects Paup*, please check carefully for the path you entered.

Getting started

At first, the PaupUp interface is very similar to the PAUP* one on Mac OS and users familiar with this version should find it straightforward to use. New users should read the PAUP* documentation if they experience problems. As previously explained, about 80% of the PAUP* commands are available through the graphical interface of PaupUp. The remaining ones are available through direct command-line text box. Commands entered here will react exactly the same way as if they were entered directly in the PAUP* DOS application. Finally, the command history window allows the user to check for commands that were actually sent to PAUP* by the interface, which could be helpful for debugging (hopefully not needed anymore!) and teaching activities. The raising demand for the implementation of Modeltest procedures in PaupUp from the beta version users is now addressed as long as the path for modeltest software is provided in the preferences options. Current version uses modelblockPAUPb10 NEXUS file that the user may find in the PaupUp installation folder. As a last tool, visualization of computed trees can be performed by clicking the ‘print trees’ option in the tree menu, which automatically launches the Treeview software with your current tree(s) if you did set the path for this software (Options Menu, Preferences).

Operating systems
Executable is provided for Windows operating systems for which user friendly interface is an issue in current PAUP* version.

Calendini, F. & Martin J.-F. 2005. PaupUP v1.0.3.1 A free graphical frontend for Paup* Dos software.

Of course PAUP* should still be cited independently as :

Swofford, D. L. 2000. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
Note: Because there are a number of beta and test versions of the program you should mention the specific version of PAUP* somewhere in the methods.

As in-text reference, we recommend citing: "Paup 4.0b10 (Swofford 2000) using PaupUp graphical interface (Calendini & Martin, 2005)".


System Requirements

  • Supported Operating Systems: Windows 98; Windows ME; Windows NT (not tested); Windows 2000; Windows XP
  • Microsoft Windows NT 4.0 requires Service Pack 6a.
  • The programming language used for PauUp is Visual Basic.NET and may require a Windows update on older computers. The Microsoft® .NET Framework version 2 redistributable package includes everything you need to run applications developed using the .NET Framework as PaupUp and can be found here.

These are some useful links and external softwares related to PaupUP:

  • Of course PaupUP is nothing without PAUP* ! Paup* Home page.
  • The integration of modeltest NEXUS block involves Modeltest.
  • Visualization of trees is made possible using Treeview software.
External ressources
The compression format used for packaging this software was the RAR file format, most commonly used on DOS/Windows machines.
  • WinRAR is a popular software package used for making RAR and ZIP files.
  • Several packages can unpack (but not pack/create) RAR and ZIP files, including PowerArchiver.


Disclaimer: The software on this page is free to download and use, and thus comes with no warranty of any kind. While it hasn't caused us any problem, current version of PaupUP is still considered as beta version and you are responsible for any damages or loss of data you may sustain while using this software.

Correspondence about this program should be addressed to Jean-Francois Martin at