NOTES ON PORTABLE BETA TEST VERSION 4.0b ============================================== INSTALLATION ---------------------------------------------- PAUP* 4.0 beta and associated files are distributed in a tarfile archive. To extract the files from the archive simply move the tarfile to the directory where you wish to install the PAUP directory and type: tar -xf paupxxxx Where xxxx is the version name. The PAUP directory contains the following files: paup4b9-xxxxx //PAUP binary Docs/Cmd_ref_v2.pdf //Command reference documentation Docs/Quick_start_v1.pdf //introduction to basic PAUP* usage Release-Notes.txt Sample_analysis_files/ML_analysis.nex Sample_analysis_files/MP_analysis.nex Sample_import_files/GCG.msf Sample_import_files/hennig86.hen Sample_import_files/mega.meg Sample_import_files/nbrf.pir Sample_import_files/phylip_3x.dat Sample_import_files/simple.txt Sample_import_files/tab.txt Sample_NEXUS_files/angiosperms.nex Sample_NEXUS_files/avian-ovomucoids.nex Sample_NEXUS_files/primate-mtDNA-interleaved.nex Sample_NEXUS_files/primate-mtDNA.nex In order to execute PAUP, the PAUP binary must be in your search path. Typing "echo $PATH" or "echo $path" will usually tell you what directories are in your search path. You can either move the PAUP binary to one of the directories already in your path or add a new directory to your search path and move the PAUP binary to the new directory. DOCUMENTATION and SAMPLE FILES ---------------------------------------------- The file "Cmd_ref_v2.pdf" is an Adobe Acrobat document containing preliminary documentation. This document is primarily a "command reference" and it is still fairly rough. The document is heavily hyperlinked and it is easy to navigate using Acrobat 3.0 or later (http://www.adobe.com/Acrobat). Newer versions of the manual will be made accessible on-line as they become available. The Quick-start tutorial is designed to introduce users with no previous experience to the basic usage of PAUP* 4. After version 4.0 is complete, a paper copy of the final documentation will be mailed to you. NEXUS formatted sample data files are provided in the Sample_NEXUS_files directory. The Sample_import_files directory contains Non-NEXUS formatted files that PAUP can import with the "tonexus" command. See the command reference document for more information regarding the "tonexus" command. Finally, two sample analysis files are provided in the Sample_analysis_files directory. To run one of these files, go to the Sample_analysis_files directory and type the name of the PAUP binary followed by the name of one of the sample files. For example: system prompt> paup4b MP_analysis.nex This example assumes that the paup binary (paup4b) is in your search path. SUPPORT ---------------------------------------------- Support for most issues pertaining to use of PAUP* can be found on-line at: http://paup.csit.fsu.edu/support.html If you are unable to find an answer to your question on one of our web pages, we encourage you to post your question to the appropriate "conference" at the PAUP*forum web site: http://pauptech.csit.fsu.edu/~paupforum/ Since we are not a giant software company with a staff of technical support specialists, posting your questions to the PAUP*forum is fastest way to get an answer to your question. Jim Wilgenbusch and I will try to answer your questions as quickly as possilbe, but our time is limited (especially given the need to complete the 4.0 program and manual). There are no restrictions on publication of results using this beta version (unlike the earlier development versions). The recommended citation format is: Swofford, D. L. 2002. 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. REPORTING PROBLEMS ---------------------------------------------- Thank you for taking a chance on this beta version. Your cooperation in reporting any bugs or other anomalies would be appreciated. Suggestions for enhancements are welcome, although, unless a feature is both extremely simple to program and very compelling, new features will have to wait until after 4.0 has been completed. If you report a bug, please be sure to supply all necessary information that will enable us to replicate it. This includes: 1. A description of the problem, including a list of all steps that led to the bug. If you can repeat the problem yourself in a well-defined sequence of steps, there is a much greater chance that I will be able to fix it. 2. A copy of the data file and any other relevant files (these will kept strictly confidential). 3. The exact version number of the program. 4. The CPU and operating system on which you are running the program. Send reports to: paup-support@csit.fsu.edu Please check our "Known Problems" page http://paup.csit.fsu.edu/problems.html before sending your bug report. There is no need to report bugs that are already known. If there is any question as to whether your bug duplicates a known problem it would be better to send it in just in case. Thanks, Dave Swofford