PAUP* 4.0 Beta: Command Reference --Draft Version 3--

PAUP* 4.0 beta version disclaimer and user agreementThe version of PAUP* 4.0 currently available is a beta version. We are notaware of bugs that would cause the program to obtain incorrect results, butthey could certainly exist. Other bugs could cause the program to terminateabnormally or misbehave in other ways. Your use of this software impliesyour acceptance of its unfinished status. We would greatly appreciatereceiving reports of any problems you encounter. Send them by email to:paup-support@csit.fsu.edu. Please include all details necessary toreproduce the problem, including: (1) type of machine and operatingsystem version; (2) specific version number of PAUP* (e.g., PAUP*4.0b8);(3) a specific sequence of operations that will cause the problem to occur,beginning with start-up of the program; and (4) a sample data file and anyother associated files that will enable the problem to be reproduced.The following license agreement and disclaimer apply both to the betacopies and to the final release version:PAUP* is licensed to individual users for the sole purpose of facilitating thescientific research of the licensee. This software may be used in more thanone location or by more than one person provided that there is nopossibility that it will be used by two or more people simultaneously.Generally, this qualification means either of the following: (1) the programmay be used by a single researcher on any number of machines in his or herpossession, or (2) the program may be installed on a single computer andused by one or more individuals who have access to that computer.THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. DAVIDL. SWOFFORD AND SINAUER ASSOCIATES DO NOT WARRANT, GUARANTEE, ORMAKE ANY REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THESOFTWARE OR DOCUMENTATION IN TERMS OF THEIR CORRECTNESS, RELIABILITY,CURRENTNESS, OR OTHERWISE. IN NO CASE WILL THESE PARTIES BE LIABLE FORANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR OTHER DAMAGES THAT MAYRESULT FROM USE OF THIS SOFTWARE.Suggested CitationPAUP* 4.0 is in many ways comparable to a monographic article. In itsapproximately 180,000 lines of code, PAUP* implements numerous originalconcepts and ideas and contains many new algorithms. For these reasons,citation of the program in a book format is recommended:Swofford, D. L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony(*and Other Methods). Version 4. Sinauer Associates, Sunderland,Massachusetts.Copyright © David L. Swofford, 1989-2002.All Rights Reserved.ii February, 2002 PAUP* 4.0 beta documentaion