PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta

David L. Swofford, Florida State University

2002
CD-ROM

About This Title

PAUP* 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, UNIX/VMS, or Windows/DOS-based formats.

WHY ARE WE SELLING A BETA VERSION?

As you probably know, PAUP* 4.0 has been under development for several years, but has been delayed for a variety of reasons. The program is nearly complete, but needs a little more work to resolve remaining interface bugs and complete the feature set. Also, the manual for the new version has not been completed. The program is probably less buggy than the vast majority of commercial software, and is ready for serious use despite the few remaining problems. We are making the beta version available as a service to those who would like to obtain a version of the program now rather than wait for the final release. We emphasize that we are not encouraging you to make this purchase now, but are simply making it available for those who would rather have a beta version than no version at all.

Due to an extensive testing program involving development (pre-alpha) versions of the program, we are not aware of any bugs that affect the correctness of the results produced. However, the demand for test versions has increased to the point that we have decided to make a beta version generally available, without the restrictions on publication that have accompanied the earlier test versions.

The beta version we are making available will allow you to continue to use the program until the final version is released. Prior to the completion of the final version, revisions may be made to the program, and updaters released. Updaters may be downloaded from the PAUP web site at paup.csit.fsu.edu. WE WILL SHIP THE FINAL VERSION TO YOU AUTOMATICALLY when it is completed, as long as we have up-to-date address information.

WHAT IS MISSING IN THIS VERSION?

Complete information regarding system requirements and version differences can be found at paup.csit.fsu.edu.

A document on the CD gives a complete description of the remaining known problems and incomplete features. The most significant of these are:

Some features of formalized NEXUS standard are still not supported, including but not limited to: + some distance- and character-matrix options + input of distance matrices in "interleaved" format
The online help file is out-of-date.
Interconversion of some foreign data-file formats has not been completed.
Needs command-line and PAUP-block support for exporting data files (portable interface versions).
Option to automatically save trees to file during searches is incomplete and is not available in this test version. When finished, this option will allow runs that terminate abnormally due to crashes, power problems, etc., to be restarted from an advanced point rather than from scratch.
Source code. When the program is finished, source code will be available for compilation and execution on any system that has a C compiler. In the meantime, a wide range of VMS and Unix binaries are available for downloading on our FTP site.
Documentation. Although there are a few instruction files on the CD, the manual is not yet available. You will need to be resourceful in using on-line help capabilities, and you can refer to the PAUP* web site for additional information.

A PREVIEW OF SOME OF THE NEW FEATURES NOW AVAILABLE IN PAUP* 4.0:

Full support for tree searching under DNA maximum-likelihood and distance-based optimality criteria (in addition to parsimony).
Automatic estimation of maximum-likelihood model parameters, either on specified trees or during tree searches. A wide range of DNA substitution models are available, including the most general reversible model and its submodels (Jukes-Cantor, Kimura 2P, HKY85, F84 used in DNAML and fastDNAml, Tamura-Nei). Among-site rate variation can be accommodated using gamma-distributed rates, an unknown fraction of invariable-sites, site-specific rates, or a combination of these.
Estimation of evolutionary distances under a full set of reversible models, including "custom" distances that can be tailored to any restriction of the most general reversible model and the LogDet distance. Distances can be corrected for among-site rate variation using gamma and invariable-sites models (or both).
Neighbor-joining, quartet-puzzling, star-decomposition and UPGMA tree-searching algorithms (in addition to stepwise addition and branch-swapping of earlier versions).
Calculation of "agreement subtrees" (largest common pruned trees) showing the largest subset of taxa for which all trees in a set agree upon relationships.
Jackknife resampling analysis under all optimality criteria (in addition to bootstrap).
Parametric and nonparametric tests for significant differences between trees (Kishino-Hasegawa, Templeton, winning-sites).
Printing of unrooted trees and support for printing large trees across multiple pages (Macintosh version only).
Tree-searching and evaluation under Goloboff's "implied weights" parsimony criterion.
Partition-homogeneity (incongruence length-difference) test for evaluating homogeneity of subsets of characters (e.g., between genes, or between molecular and morphological characters).
Estimation of ancestral nucleotides using maximum likelihood.
"Portable interface" version for DOS (including MS Windows), VMS, and Unix operating systems.

PAUP* 4.0 beta version disclaimer and user agreement

READ THIS BEFORE PURCHASING PAUP* 4.0 BETA VERSION. YOUR PURCHASE AND SUBSEQUENT USE OF PAUP * 4.0 BETA VERSION, or PAUP* 4.0, INDICATES YOUR ACCEPTANCE OF THE TERMS OF THIS DISCLAIMER AND OF THE USER’S AGREEMENT.

The version of PAUP* 4.0 currently available is a beta version. We are not aware of any bugs that would cause the program to obtain incorrect results, but they could certainly exist. Other bugs could cause the program to terminate abnormally or misbehave in other ways. Your use of this software implies your acceptance of its unfinished status. We would greatly appreciate receiving reports of any problems you encounter. Send them by email to: paup-support@csit.fsu.edu.

Please include full details necessary to reproduce the problem, including: (1) type of machine and operating system version; (2) specific version number of PAUP* (e.g., PAUP*4.0b1); (3) a specific sequence of operations that will cause the problem to occur, beginning with startup of the program; and (4) a sample data file and any other associated files that will enable the problem to be reproduced. You may wish to check under known problems at the PAUP* website (paup.csit.fsu.edu) before sending in your bug report. There is no need to report a bug that has already been reported, but if there is any question as to whether your bug duplicates a known problem it is better to send it just in case.

The following license agreement and disclaimer apply both to the beta copies and to the final release version:

PAUP is licensed to individual users for the sole purpose of facilitating the scientific research of the licensee. The software may be used in more than one location or by more than one person, provided that there is no possibility that it will be used by two or more people simultaneously. Generally, this qualification means the following: (1) the program may be used by a single researcher on any number of machines in his or her possession, or (2) the program may be installed on a single computer and used by one or more individuals who have access to that computer.

THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. DAVID L. SWOFFORD, THE SMITHSONIAN INSTITUTION, AND SINAUER ASSOCIATES DO NOT WARRANT, GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THE SOFTWARE OR DOCUMENTATION IN TERMS OF THEIR CORRECTNESS, RELIABILITY, CURRENTNESS, OR OTHERWISE. IN NO CASE WILL THESE PARTIES BE LIABLE FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR OTHER DAMAGES THAT MAY RESULT FROM THE USE OF THIS SOFTWARE.

IMPORTANT NOTE ABOUT THE MACINTOSH VERSION: The GUI version of PAUP* requires either Mac OS 9, or Mac OS X (pre-10.5, non-Intel) with Classic installed. For more information, please go to the FAQ page of the PAUP* website, and read the "Questions about PAUP* interfaces" section.
Also: The Macintosh version now includes the command-line version for Mac OS X (as well as the standard GUI Macintosh version).

NOTE FOR INTEL MAC USERS: Intel Mac users must use the command line version included on the CD. If you have an older version of the PAUP* CD, please contact support@sinauer.com for download instructions. When emailing, it will help to expedite the process if you include as much as possible of the following information: when the purchase was made, where it was purchased, where it was shipped to, the invoice number, and the program serial number.

IMPORTANT NOTE ABOUT THE WINDOWS VERSION: The Windows version of PAUP* runs as a "GUI" application, however, unlike the Macintosh version, it is command-line-driven. The advantage to running PAUP* under Windows as opposed to DOS is that a scrollback display buffer is built into the program, an editor is provided, and commands are remembered between sessions (they can be recalled, edited, etc.). Also note that PAUP*4.0 Windows does not print or save high-resolution trees. (However, these can be printed using free third-party software.)

Site License Information

PAUP* is also available for simultaneous use on multiple machines. For more information, download the site license agreement and the site license fee schedule. Orders for site licenses must include a signed site license agreement, and may be faxed to: Marie Scavotto at 413-549-1118. Questions may be directed to scavotto@sinauer.com.

Pricing and Options

Titles	Product Code	Price (USD)
*PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta for Windows/DOS (No Manual)**	0-87893-807-9	$85.00	Purchase
*PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta for Macintosh (No Manual)**	0-87893-806-0	$100.00	Purchase
*PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta for Linux/UNIX (No Manual)**	0-87893-804-4	$150.00	Purchase
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