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PAUP* 4.0 Beta: Command Reference --Draft Version

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* Phylogenetic Analysis Using Parsimony * and other methods Version 4.0 beta version David L. Swofford Beta Documentation This documentation is currently under construction, therefore, we cannot guarantee the accuracy of the information described herein. A much more user-friendly manual is in progress. Revisions will be made available to registered users over the World Wide Web at http://paup.csit.fsu.edu. A list of frequently asked questions is also available at this website. Many of the commands and options described in this document are hyper-linked to facilitate and promote on-line use until a final draft is complete. Comments regarding this document should be addressed to [email protected]. PAUP* 4.0 beta version disclaimer and user agreement The version of PAUP* 4.0 currently available is a beta version. We are not aware of 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: [email protected]. Please include all details necessary to reproduce the problem, including: (1) type of machine and operating system version; (2) specific version number of PAUP* (e.g., PAUP*4.0b8); (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 any other associated files that will enable the problem to be reproduced. 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. This 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 either of 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 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 USE OF THIS SOFTWARE. Suggested Citation PAUP* 4.0 is in many ways comparable to a monographic article. In its approximately 180,000 lines of code, PAUP* implements numerous original concepts 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 Table of Contents TABLE OF CONTENTS Table of Contents .................................................................................1 Command Reference ...........................................................................5 Command Format................................................................................5 Identifiers ............................................................................................................................... 6 Common Command Elements............................................................................................ 8 Commands used in the TAXA Block ..............................................10 Dimensions .......................................................................................................................... 10 TaxLabels.............................................................................................................................. 10 Commands used in the CHARACTERS Block ..............................11 Dimensions .......................................................................................................................... 11 Format................................................................................................................................... 12 Eliminate .............................................................................................................................. 15 TaxLabels.............................................................................................................................. 16 CharStateLabels................................................................................................................... 16 CharLabels ........................................................................................................................... 16 StateLabels ........................................................................................................................... 17 Matrix.................................................................................................................................... 17 Commands used in the DATA Block..............................................18 Commands used in the ASSUMPTIONS Block.............................19 Options ................................................................................................................................. 20 UserType .............................................................................................................................. 20 TypeSet ................................................................................................................................. 21 WtSet..................................................................................................................................... 21 ExSet...................................................................................................................................... 22 AncStates.............................................................................................................................. 22 Commands used in the SETS Block.................................................22 CharSet ................................................................................................................................. 23 TaxSet.................................................................................................................................... 24 CharPartition, TaxPartition ............................................................................................... 24 Commands used in the TREES Block..............................................25 Translate ............................................................................................................................... 25 Tree........................................................................................................................................ 25 Commands used in the CODONS Block........................................27 CodonPosSet........................................................................................................................ 27 PAUP* 4.0 beta documentaion February, 2002 1 Table of Contents Commands used in the DISTANCES Block...................................27 Dimensions .......................................................................................................................... 28 Format................................................................................................................................... 28 TaxLabels.............................................................................................................................. 30 Matrix.................................................................................................................................... 30 Commands used in the PAUP Block...............................................30 Options And Subcommands Affecting Multiple Commands..................................... 30 ?.............................................................................................................................................. 33 ! .............................................................................................................................................. 33 Agree..................................................................................................................................... 33 AllTrees................................................................................................................................. 35 Ancstates .............................................................................................................................. 36 Assume ................................................................................................................................. 36 BandB.................................................................................................................................... 37 BaseFreqs.............................................................................................................................. 39 BootStrap.............................................................................................................................
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