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Beta 10 Updaters
Command Reference Document
Quick Start Tutorial
PAUP Font File
CED DOS helper

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Macintosh Updaters:

The Macintosh Active and Normal updaters listed below will update any Macintosh version of PAUP* 4.0 beta to the latest beta release (beta 10). After downloading the updater that best matches your needs, double-click the updater application and follow the instructions. The updaters are stand-alone applications that are distributed in MacBinary and BinHex formats*.

Normal updater
Macbinary (2.6 MB)* The normal updater contains all the data needed for any Mac Update.
BinHex (3.6 MB)*

Stand Alone updaters (BinHex format)
The updaters listed below can be downloaded, saved on a 1.44 MB floppy diskette, and transferred to a Macintosh that is not connected to the network. We recommend downloading the Active updater if you are updating PAUP* beta on a machine that is connected to the internet.
68K no FPU (850 KB) Will update the Mac 68K no FPU version of PAUP*. Use this updater if you are running PAUP* under Executor.
68K ( 820 KB) Will update the Mac 68K version of PAUP*.
PPC (1 MB) Will update the Mac PPC version of PAUP*.
Altivec (G4) ( 1 MB) Will update the Mac Altivec (G4) version of PAUP*.
68K no FPU to PPC (1 MB) Will convert the Mac 68k no FPU version of PAUP* to the PPC version.
Altivec (G4) to PPC ( 970 KB) Will convert the Mac Altivec version of PAUP* to the PPC version.
PPC to Altivec (G4) Will convert any PPC version of PAUP* to the Altivec version.

*If you are downloading the updater to a Mac, either format will work but the MacBinary file will download more quickly. If you are transferring the file from a PC to a Mac you should download the updater in the BinHex format. To decode these files automatically you must have a "helper" utility set up in your web browser. If your web browser is not set up with a helper, download the updater and then use a decoding utility to decode the file manually. Utilities that will decode MacBinary or BinHex files are freely available on the internet (e.g., Stuffit Expander).

PC Updaters:
To get the Windows updater simply click on the corresponding link and save the updater on your harddrive; no helper is required.

Windows Interface

For BETA 6 or later

If PAUP* 4.0 Beta 6 or a later beta release is installed on your system use this updater. Win 95, 98, ME, NT, and 2000
Windows Interface

For BETA 5 or earlier

If PAUP* 4.0 BETA 5 or an earlier beta release is installed on your system use this updater. Win 95, 98, ME, NT, and 2000

Portable Version:

Unix/Linux/VMS users can download a tar archive of Beta 10 from the Portable Version download site (Note: Prior registration is required to access this site). Requests for new orders should contact Sinauer Associates, Inc.

Command Reference Document - Second Draft

Cmd_ref_v2.pdf is the latest draft of the "command reference" document. The pdf gives brief a brief description of the command and options available in PAUP*, the menu equivalent for commands, and includes examples and cross referencing. We will periodically update this document so you may not want to print these pages until we are closer to a final draft. The document contains an index and is hyperlinked throughout making it fairly easy to use on-line.

You'll need the Acrobat Reader 4.0 or greater to view this document.

Quick Start Tutorial

A hands-on tutorial briefly demonstrating the basic usage of PAUP* 4.0. Note: This is a draft version. Comments are welcome; send to:

You'll need the Acrobat Reader 4.0 or greater to view this document.

PAUP 3.1 Manual

The User's Manual for version 3.1 of PAUP.

DISCLAIMER: The information contained in this document is out of date with the respect to VERSION 4.0 of PAUP*. While the background information might be useful, the command syntax used by VERSION 4.0 of PAUP* has changed considerably and may not be compatible with what is described in the VERSION 3.1 User's Manual. See the command reference document for the VERSION 4.0 command syntax.

You'll need the Acrobat Reader 4.0 or greater to view this document.

PAUP font file

The Macintosh PAUP font File. You have two choices of where to install this file, in the system or in the same folder as the application file. We recommend that you place it in the system folder (see below for how); this seems to be best for trouble-free background printing under all configurations of the operating system and the various printer drivers. To install the font file in the system folder use one of the following methods:

  • System 6.0.x and earlier: You must use Apple's Utility program "Font/DA Mover" to install the font into the system file. The Font/DA Mover program is located on one of the disks which you use to install the system.
  • System 7.0.x and later: You can simply drag the icon of the font onto the icon of the system folder.

CED Command-line editor for DOS

If you are using DOS, we strongly recommend using the public domain command-line editor CED, which provides command-line editing and recall capabilities within PAUP*.


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