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News

04Mar02

After releasing Beta 10, we received several reports that there were also problems with beta 10. Click here for a list of known problems and possible short-term work-arounds. Because these problems are not as serious as the problem caused by the Altivec compiler (described below), we will continue to make the Beta 10 updaters available while we fix the problems reported to date. If you downloaded the 4.0b9 PPC/Altivec version, it is imperative that you replace it with the newer version!

We plan to release another beta this week that will fix the problems reported so far. If you discover any problems with Beta 10, please report them to us as soon as possible so that we can fix them before the next release.  

Many thanks for your patience and a special thanks to everyone who reported problems in beta 9/10.

03Mar02

Due to a problem with the Metrowerks C compiler, the PPC/Altivec version of 4.0b9 had a serious problem affecting likelihood analyses for which we have found a workaround. Also, a version-numbering glitch was preventing default settings and command-history from being remembered between runs. For these reasons, we have released version 4.0b10 to replace 4..0b9. If you downloaded the 4.0b9 PPC/Altivec version, it is imperative that you replace it with the newer version!

Unix/Linux and Mac OSX binaries for 4.0b10 are now available for download at the usual location.

01Mar02

Beta 9 updaters for Macs and PCs are available for immediate download at:

http://paup.csit.fsu.edu/downl.html

Updates for the Portable version (Unix/Linux) will be posted tomorrow (they do not expire for a few more days).

Beta 9 includes several new features and a number of bug fixes. A few ofthe new features include:

  • It does NOT have an expiration date!
  • Users of the Unix/Linux versions will be pleased to discover that the program now includes command-line editing and recall, with the command- history being remembered between runs. Just use the up/down arrow keys to recall previous commands, or the left/right arrow keys to move around within a command.
  • Olivier Gascuel's BioNJ method is now provided (thanks to David Bryant for help with this).
  • A new predefined exclusion-set "InfOnly" facilitates exclusion of uninformative characters, especially after excluding or excluding taxa.
  • A new predefined character-set "AllMissing" was added to quickly select all characters that have only gap/missing values in all taxa (this situation often arises when deleting taxa from a large matrix containing many characters with gaps).
  • A cleaner, more compact format is now used for output of likelihood scores and parameter estimates using the LScores command.
  • An option has been supplied to output the mean length of trees output using the PScores command, which is helpful in the calculation of partitioned Bremer support measures.

See the release notes for a complete list of new features, bug fixes, and other changes:

http://paup.csit.fsu.edu/release.html

We have decided to make this the penultimate beta release before version 4.0 becomes final. Few significant changes other than bug fixes will be made, but a few additional items need to be completed (mainly involving file import/export and remembering of parameter estimates to avoid long reoptimization waits). The only exception is that we may decide to open up some new heuristic search methods (e.g., Nixon's "parsimony ratchet") that have been frequently requested; these have been coded but need some more work before they can be included in the official version. If we don't get them into the final beta (1-2 months), they will be available in the "bleeding-edge" version mentioned in our previous message. We hope to have the bleeding-edge version ready for downloading by June or July.

28Feb02

Beta 9 updaters will be posted Friday, 1 March. We are aware that this is a day after the Mac and PC beta 8a expiration date, however, because the beta 9 update will be non-expiring, we are trying to tie-up as many loose ends as possible. To be notified as soon as new updaters are available for download subscribe to the paupinfo email list.

15Jan02

Beta 8a Expiration Patch

Our plan for the next update was to release a final, non-expiring beta version 9 prior to the expiration of 4.0b8. Unfortunately, we are still not quite there. Consequently, we have no choice but to re-release 4.0b8 (as 4.0b8a) with an extended expiration date of February 28, 2002. Updaters are available at http://paup.csit.fsu.edu/downl.html for MacOS and Win32. Recompiled Unix binaries are also available; you may download and install them using the same procedures you used earlier.

We are very close to having 4.0b9 completed, and will be posting it by the end of this week. If you can live without PAUP* for 2-3 days (or don't mind back-dating your computer long enough to start PAUP*), you may prefer to just wait until 4.0b9 is available rather than downloading the 4.0b8a updater.

A word about the status of future PAUP* development...

The next beta version will not have an expiration date, and will be the final beta version prior to the long-awaited official release of 4.0. As soon as 4.0b9 is released later this week, the source code will be forked and 4.0 will remain stable thereafter; important bugs will be fixed but no other changes will be made. This will stop the cycle of new bugs being introduced as features are added or the source code is restructured to support development of future versions. Since the program will no longer be changing rapidly, it will also give us some breathing room to make a serious run at completing the manual. Soon, we will begin making a "thrill-seekers" version available free-of-charge to those who have purchased the official version. These version will include some new features that have been programmed but are not enabled in the 4.0 betas, will be updated frequently, and will have expiration dates. Features new since 4.0 will not be officially supported, although we will continue to accept and encourage bug reports and suggestions. Once these new features are fully implemented and thoroughly tested, they will be released as part of a new, stable, non-expiring version available as an upgrade to 4.0.

We hope that by maintaining both a stable version and a bleeding-edge version we can accommodate the needs of those who want reliability and guaranteed uninterrupted availability, while continually adding new features and capabilities for those who are willing to put up with some inconvenience and annoyance. Features that will be coming in the bleeding-edge versions include parsimony-ratchet and other new heuristic search strategies, partitioned maximum likelihood analyses, maximum-likelihood for morphology (using Paul Lewis's method), automated model selection entirely within PAUP*, parametric bootstrapping and other simulation analyses, more complex DNA substitution models, support for parallel clusters using MPI and PVM, multithreading for dual and quad-processor machines, and imbedded Python scripting. We cannot promise exactly when any of these features will be available (and you wouldn't believe any promises we made anyway), but significant progress has been made on all of them and we will make them available as soon as we can.

Again, we thank you for your patience and understanding as we try to complete PAUP* 4.0. We recognize that mistakes have been made, but these have always been due to our all-consuming desire to improve the program--we just haven't been very realistic about how long things would take. It's really quite a large undertaking and we are doing the best we can with limited resources. We're trying to learn from our mistakes and ask that you please bear with us just a little while longer.

Dave Swofford
Jim Wilgenbusch

16Jul01

PAUP* Moves to FSU

After 9 years at the Smithsonian Institution in Washington, D.C. David Swofford, the author of PAUP*, is moving to Tallahassee, Florida to join the Faculty of Florida State University (FSU) in the School of Computational Sciences and Information Technology (CSIT). The move promises to be a great opportunity for Dave to interact with scientists in both computational and biological disciplines. The only immediate change that PAUP* users will notice as a result of the move will be the location of the official PAUP* web site (http://paup.csit.fsu.edu), the email address for PAUP-support (paup-support@csit.fsu.edu), and the PAUP email lists (coming soon). Jim Wilgenbusch is also moving to FSU from the Smithsonian to continue his role in the support and development of PAUP*. Sinauer Associates, Inc. will continue to distribute PAUP* 4.0 beta.

29Mar01

The saga continuezzz...

In our ongoing effort to produce a stable, near-final beta version, we are releasing 4.0b8 to correct some significant problems that were either new to 4.0b7 (unanticipated side-effects of a different bug fix) or were unknown to us at the time 4.0b7 was released.

The most important issues corrected in this version include:

  • Completely broken bootstrap with neighbor-joining search: all bootstrap values were being reported as 100% (new to 4.0b7)
  • Possible incorrect tree-length calculation with asymmetric stepmatrix characters, sometimes resulting in suboptimal trees being saved rather than optimal ones (old)
  • Refusal to do bootstrap with non-integer weights when using parsimony criterion (new to 4.0b7)
  • Incorrect behavior of constraints in Altivec version when constraint tree had more than 32 internal nodes (old)
  • Crashing when "parsimony-based approximations only" was requested with the Likelihood Scores (LScores) command (new?)
  • Crashing or other misbehavior when doing "full" or "RELL" significance probability evaluation for K-H and S-H tests with data sets containing a mixture of nucleotide and non-nucleotide characters (old)

As always, more detailed description of the changes is available in the release notes file.

The Beta 8 Updaters are available at the dowloads site.

In almost all cases, the problems corrected in this version will either cause a crash or will produce obviously incorrect results. Nonetheless, it is important that you replace 4.0b7 with this version, although it will not generally be necessary to repeat previously conducted analyses unless you were doing one of the things listed above.

21Mar01

PAUP BETA 7 is available

We have released another update that fixes a few remaining problems that were not detected until after 4.0b6 was posted. You can download an updater from our download site.

The most significant bug fixes include:

  • Incorrect calculation of HKY and "custom" distances when removal of a proportion of constant sites was also requested.
  • Crashes or refusal to continue when maximum-likelihood distances were used in any context and a distribution of rates was requested (gamma, invariable-sites, or both)
  • Failure of branch-and-bound search to save any trees under least-squares distance criterion.
  • Intermittent Windows version crash when "Edit Display Buffer was chosen from the Edit menu.
  • Inappropriate insertion of "#NEXUS" into the middle of files when a PAUP-generated file was appended to an existing file in Windows version.

See the release notes file for additional fixes and more details. Although these problems are generally not as serious as the ones that were fixed by version 4.0b6, we urge all users to update to this latest version.

We finally had a chance to build portable-version binaries for Unix and VMS systems. Many platforms are now supported:

  • Compaq Alpha: Tru64 Unix and Linux; 21164 (ev5) and 21264 (ev6) processors
  • Alpha systems running under the VMS operating system
  • IBM RS/6000 running under AIX (includes SP2 systems)
  • Silicon Graphics (SGI) running under IRIX; MIPS II and MIPS III processors
  • Sun SPARC systems (binaries for generic processors as well as optimized versions for 32- and 64-bit UltraSPARC systems)
  • x86 Linux
  • PowerPC Linux
  • MacOS X (portable-interface/command-line version). We do not yet have a Carbon or Cocoa version, but the PPC and Altivec MacOS versions run fine under the MacOS X beta.

The bug-report rate has slowed to a trickle, so we think this version should be stable. We will continue to fix problems as they come in and provide updates if necessary, however, so please report any bugs or other anomalous behavior that you encounter.

1Mar01

BETA 6 Release

As you undoubtedly already know, the beta version of PAUP* posted last week (4.0b5) had major problems. A number of bugs were introduced in the process of making several "infrastructural improvements" to the program, and due to the expiration we did not have much time for in-house testing. A new version (4.0b6) is now available; updaters are available at the PAUP* download site. We will release the Unix binaries the week of March 4th. We believe most of the problems have now been corrected, but if not, let us know and we'll keep working on it until we get it right.

Because of the severe nature of many of these problems, you should not continue using 4.0b5, and you should repeat analyses using the new version before publication of any results. Even if the program didn't crash, you shouldn't believe the results. Here is a brief list of the most significant bugs that were fixed; please refer to the release notes for more detail.

  • Bootstrap crash with DNA-specific analyses (both distance and ML)
  • Crash when performing ML analyses that required single-site likelihoods (e.g., K-H or S-H tests) if a previous LScores command had been issued
  • Crash with symmetric stepmatrix characters at initialization time
  • Crashes or other misbehavior when characters that were "missing" for all non-deleted taxa were used in ML analyses
  • Failure to re-initialize the counter for the total number of included sites in DNA-specific analysis caused bogus results in several contexts, such as ML analyses with estimation of the proportion of constant sites, boostrapping and jackknifing, etc.
  • Omission of the estimated R-matrix from the ML score file, which among other things made the file incompatible with David Posada's ModelTest program
  • Failure of branch-and-bound search to save any trees in some cases.
  • Crash after showing frequency distribution of tree scores forom exhaustive search or evaluation of random trees
  • Crashing when showing the relative probabilities of each base assignment in ML character-state reconstructions after one or more characters had been excluded
  • Inappropriate retention of suboptimal trees in distance analyses when the option to collapse zero-length branches was requested.

22Feb01

Unfortunately, for every improvement made and new feature added to PAUP* comes the potential for new problems. Over the last week we have received numerous reports from users demonstrating this point with beta 5. Please be assured that we are working to fix the problems and hope to have a patch available soon. In the meantime, if you encounter a problem, please check our known problems site to see if the bug has already been reported. If it has, there is no need to report it again. If you have any doubts about whether the problem you are experiencing has been reported, please don't hesitate to send an email to paup-support describing the problem (see the support site for a list of information we will need to process your report as efficiently as possible). As soon as a patch for beta 5 is available we will send a message to the paupinfo email list.

Thanks for your patience,

Jim

17Feb01

BETA 5 IS OUT!

A new beta version of PAUP* 4.0 is now available!

If you currently own a Macintosh or Windows/DOS beta versionof PAUP* 4.0 you may download an updater application now to update your existing beta.

Note: Unix users will receive another message with instructions for downloading a beta 5 archive.

In addition to bug fixes, beta 5 includes a number of new features and enhancements; such as,

  • The Shimodaira-Hasegawa test for a posteriori comparison of tree topologies under the likelihood criterion.
  • New choices of test distributions for the Kishino-Hasegawa test under the likelihood criterion (full bootstrap and RELL).
  • Greatly sped up the optimization of likelihood substitution-model parameters when more than one parameter was estimated (e.g., TRatio and Pinvar) and the clock-constraint was in effect.
  • Greatly sped up likelihood tree-searching, especially when a gamma-distributed-rates model is used.
  • Optimization for the Macintosh G4 processor, speeding parsimony searches by up to a factor of two.
  • Sped up the calculation of tree scores under minimum-evolution and least-squares criteria, especially when enforcing branch-length-nonnegativity constraints (new methods developed in collaboration with David Bryant).

For a comprehensive list of bug fixes and new features available in beta 5 please see the beta 5 release-notes.

With the release of beta 5, we are also making available a revised command-reference document and a first-draft of a quick-start tutorial. The command-reference revision provides a brief description of the new features available in beta 5, gives the menu equivalence for commands, and includes examples and cross referencing. The quick-start tutorial is designed to introduce users with no previous experience to the basic usage of PAUP* 4.0. All of thePAUP* 4.0 interfaces are discussed in the tutorial. The revised command-reference document and the quick-start tutorial are available on our download site.

Finally, we wish to again thank everyone who reported bugs and gave suggestion for improving PAUP*. Version 4.0 of theprogram and documentation are close to being complete and we are certain that despite the inconveniences of updating and the lack of documentation, PAUP* 4.0 will be better program because of your input.

Sincerely,

Dave Swofford
Jim Wilgenbusch

16Feb01

The new beta versions are within a few hours of completion. We will be posting the updater to the web site this afternoon. I apologize for the lapse, but because of other commitments it was necessary to work right up to the last minute (I am writing this at 3am). I need to take a few weeks off from PAUP* programming, and didn't want to produce yet another interim release that would have to be replaced soon.

I think you will be happy with the new beta. Thanks for your patience. I hope you will believe that I am doing the best that I can.

Dave Swofford

23Jan01

Beta5 is no yet finished, however, we hope to have it ready by the first week of February. An email announcement will be sent to the list of registered users the moment it is available. In the meantime, we have created an updater that will extend the life of the Macintosh and Windows versions 4.0b4a by one month (to15 Feb.). This updater is now available at our download site. The updater will only update version 4.0b4a (if you have never updated 4.0b4 to 4.0b4a, you will need to do this first).

Unix users may obtain an archive containing the beta with the extended expiration date using the same set of instructions that were originally mailed to you.

If you are unable to download the udpater you can still run the earlier versions by backdating your system clock. The only time the date is checked is when the program first starts, so after PAUP* is running you can restore your system to the correct date. Some users may find this solution more convenient than having to download and apply two updates.

5Jan01

BETA 5 IS COMING

While beta 4a has been a stable release, it has served its purpose and will expire at the end of January 15, 2001. However, before beta 4a expires, we will post Macintosh and Windows updaters to the PAUP* download site and send a message to the paupinfo e-mail list. To keep the size to a minimum, the new updaters will only update the beta 4a release. If you have an earlier beta, then you will need to update to beta 4a first and then to beta 5. In addition to bug fixes, beta 5 will include a number of new features. Accordingly, we hope you will look at the upcoming release as a free upgrade rather than as another annoying expiration :-).

UNIX/VMS beta 4a users will be sent special instructions for downloading an archive file containing the new Beta 5 binary.

Note: Analyses started before 16 January will continue to run through the expiration date. PAUP* checks the expiration date only when the program is started. Therefore, if for any reason you cannot download the new updater before the expiration date, just backdate your computer, and start PAUP*. After PAUP is started you can reset your computer's clock to the correct date.

24Feb00

UNIX/VMS beta builds are available!

If you have already purchased a license for the portable version of PAUP* you will receive an email message with instructions for downloading one of the portable binaries. Please disregard this message if you are not interested in installing the beta version on your system or there is not a binary currently available for your platform. If you cannot run one of the precompiled binaries listed below and want to run PAUP* now rather than continue to wait for the source-code distribution, let us know. Requests for new orders should contact Sinauer Associates, Inc.

  • Alpha/Unix (Linux, OSF1, Digital Unix, Tru64 Unix)
  • Alpha/VMS
  • PPC/Linux
  • x86/Linux
  • SPARC - UltraSPARC/Solaris
  • SGI/Irix
  • Possibly others on request

9Feb00

Beta 4a replaces Beta 4

We received a few reports of problems with beta 4 and decided to post an updater to fix these problems sooner rather than later. Although the problems with beta 4 are minor, we suggest that all users update to the new version (beta 4a). There is no urgency to do so, nor any need to repeat analyses run with 4.0b4. The changes made between beta 4 and 4a are outlined in the PAUP* release notes.

Now that several "unexpired" beta releases are in circulation, we ask that you pay close attention to the release you are using before reporting a bug. We are only interested in bugs that can be reproduced under the latest beta version (Beta 4a). We also encourage you to look at the "Known Problems" site before reporting a bug. If a problem has already been reported, there is no need to report it again. 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.

7Feb00

BETA 4 replaces Beta 3/3a!

A new beta version is now available for downloading. This version corrects a few additional problems that were discovered after the release of 4.0b3a. Most of these problems were system/configuration specific, so it took a few days for the bug reports to roll in and for us to correct the problems.

The two most common problems were refusal to execute files selected from the Open dialog box in the Windows 95/98/NT version and crashing of the Macintosh version during heuristic and branch-and-bound searches on MacOS system versions older than 8.5 (and possibly later systems as well). The first problem only occurred if the option to hide extensions for registered file types was enabled (we want to see those extensions, so we always turn this option off). The second problem was due to an incompatibility accidentally introduced while consolidating Mac and Win32 status-window code in an attempt to simplify cross-platform development.

Another serious problem with 4.0b3/4.0b3a was in the quartet-puzzling method. You should repeat any runs in which approximate likelihoods were used in evaluating quartets (which is the default setting).

A few other problems were corrected, and we believe that this version will be very stable. More information on the changes in this version is available in the release notes.

18Jan00

Important Update to BETA 3!

Shortly after the release of beta 3, several users sent in reports that the new beta version was crashing. The problem resulted from memory corruption that occurred if you started the program with an indirect launch (i.e., double-clicking a document or by dragging a document icon onto the application icon) and then initiated execution from an open editor window. This sequence led to all sorts of crashes, freezes, and anomalous results either immediately or at some later time. The crashes were important enough that we decided to release another updater. If you are currently using beta 3 or any earlier beta version you should UPDATE TO BETA 3a NOW. Licensed users may upgrade any earlier beta version by downloading an updater from this site.

The beta 3a updater also corrects a problem that caused unparsimonious trees to be saved when using stepmatrix characters with non-integer costs.

Beta 3a still provides program enhancements and fixes problems that surfaced since the second beta. Here are a few of the new features included in the beta 3/3a release:

  • Trees may now be filtered according to the best tree score.
  • Option to output the posterior probability that a site belongs to a given rate category (maximum-likelihood models with gamma and invariable sites models).
  • Standard errors for maximum-likelihood branch length estimates.
  • A likelihood-ratio test to evaluate whether each branch-length is significantly greater than zero.
  • Option to add a title to each page output by the "Print Trees" command (Mac only).
  • Option to save trees to a file in "matrix representation."
  • Option to write user-supplied branch lengths with trees saved to files.
  • Option for outputting tree scores to a text file under parsimony and distance criteria.
  • Option to export data to the NEXUS format.
  • A command-line interface to the "Export Data" command.
  • Files may be opened for editing using a drag-and-drop operation to PAUP's main window.
  • Several enhancements to the Windows 95/NT version, including support for printing, editing the display buffer, search-and-replace in the editor, and a Window menu that lists all open files. Calculations are also now much faster in the Windows version.

Please see the release notes for more information on what is new in beta 3a, and for a full list of the bug fixes. Requests for new orders should contact Sinauer Associates, Inc. Many thanks to everyone who gave suggestions and reported problems with previous beta versions.

24Nov99

PAUP* forum

In response to the growing number of technical questions submitted to paup-support, we've created a Tech Exchange site call "PAUP* forum". "PAUP* forum" is divided into interactive conferences covering such topics as, how to use PAUP, and general issues pertaining to phylogenetics. Users may participate in "PAUP* forum" conferences through a web browser, news reader, or email program. See the "PAUP* forum" online help for more details about participating in conferences.

16Apr99

IMPORTANT MESSAGE TO RECIPIENTS OF BETA-2 DISKETTES!

We have just discovered that the serial numbers attached to the PAUP* beta-2 diskettes recently shipped by Sinauer Associates were printed incorrectly. As a result, the personalization dialog refuses to accept the serial number as provided. Here is what you need to do to convert the serial number you received to a valid serial number:

Replace "BP " with "B" (note that the new serial number contains no spaces).

Replace the first two numeric digits with "41".

Enter the remaining digits exactly as given.

This modified serial number should be accepted by PAUP*. If you still have problems, contact paup-support@lms.si.edu. Please accept our apologies for this inconvenience.

5Apr99

Over the last week we received several reports concerning problems with beta 2. These problems were serious enough that we have decided to release an update right away--IT IS IMPORTANT THAT YOU CONVERT YOUR CURRENT VERSION using a new updater now, which will convert your "paup4b2" program into "paup4b2a".

The most serious problem sometimes resulted in treelength miscalculations during heuristic searches under the parsimony criterion. This miscalculation sometimes caused an apparent "hang" as the program kept finding trees of impossibly short length. In other cases, the treelength or Goloboff-fit reported at the end of the search differed from the value obtained from "Tree Scores: Parsimony" (PSCORES) output.

This updater also corrects problems that caused the 68K version to erroneously complain about insufficient memory when using stepmatrices, and fixes tree-printing problems that occurred with some versions of the LaserWriter driver.

Also, the Win32 version of the second beta is now available; the latest updater will update your copy of the first beta version to the second.

For those who are still waiting for your copies to be delivered--we have just sent the latest beta version to Sinauer Associates and they will be duplicating and mailing these out over the next few days.

Please keep checking the web site for further developments.

Dave and Jim
Your dedicated (and tired) PAUP* support team

31Mar99

In my rush to do the final builds of beta 2, I neglected one trivial detail that can have potentially serious implications. Namely, I forgot to set a flag that would cause the preferences file for the first beta version to be deleted and replaced by a new one specific to beta 2. The resulting mismatch between preference and application files can cause the default settings of variables to be completely inappropriate. The most severe problem is that the new "reconnection limit" feature is initially set to "1", which means that TBR branch swapping will correspond exactly to nearest neighbor interchanges (NNI).

If you downloaded the updater after 18:15 EST US, March 31 then you do not have to worry about this problem. If you downloaded the updater before this time then you will need to make a fix. To correct the problem, you must manually trash the "PAUP 4.0 Preferences" file from the Preferences folder contained within the System folder. After doing this, PAUP* will start up with the "factory default" settings the next time you run it.

We have replaced the updater on the web site with a corrected version that will update any of the previous beta versions (including the one posted yesterday). If you have already downloaded and applied the updater posted yesterday, it is probably simpler to manually delete the preferences file than to download and apply the new updater, but either solution is acceptable. It is critical that you do one or the other, though.

Other than the preferences-file issue, the only other change is that I fixed a problem that was causing the 68K version (noFPU) to crash under Executor, a program that allows (some) Macintosh software to run under Windows 95/98/NT and Linux. PAUP*/Mac runs surprisingly fast within Executor on Pentium machines (although not as fast as on a PowerMac). The only problems I have detected involve cosmetic anomalies with the menus and misplaced taxon labels in printed trees. Note that we will not be able to provide technical support for running PAUP* under Executor, however.

Sorry for the added inconvenience, even if minor. Let us know if you encounter any other problems.

Dave Swofford

30Mar99

Hello PAUP* 4.0 Beta User,

PAUP* Beta 2 for the Macintosh and DOS is complete! In additions to bug fixes, many internal aspects of the program have been changed making the Beta 2 update a major program upgrade (see Release Notes for details). If you are currently using PAUP* 4.0 Beta 1 you should update your program to PAUP* 4.0 Beta 2 by applying the latest Updater. The Beta 2 Updater will update both b1 (expiration Jan15) and b1a (expiration Feb20) programs to Beta 2. To be sure that Beta 2 will not expire without a replacement we've set the expiration date to January 15, 2000.

Dave is still working on a few bugs affecting the Windows interface; therefore, we will not be able to release an updater for the Windows version at this time. In the meantime PC users can update the DOS version of beta 1. We hope to have the Windows version ready by the end of this week.

If you are waiting for your PAUP* 4.0 beta order to be filled, we will send diskettes with PAUP* 4.0 Beta 2 to Sinauer tomorrow. Once Sinauer receives the disks they will start to fill outstanding orders. Your patience is greatly appreciated. Now that Beta 2 is complete, we plan to focus on completing the PAUP* 4.0 documentation and fixing any bugs that might have been introduced with this latest beta. We are hopeful that by summer we will be ready to ship the final version of PAUP* 4.0 with full documentation. Many thanks to everyone who has reported bugs.

Jim Wilgenbusch
paup-support

27Mar99

Alas, Beta 2 is nearly complete! Dave has finished the code and we are now in the process of running tests to make sure that everything is working properly. We will continue testing over the weekend and by Monday or Tuesday of next week we expect to post the beta Updater and send beta 2 diskettes to Sinauer so that they can begin to fill existing backorders. As soon as Beta 2 is complete we will send another message to this list. We are sincerely sorry for any inconveniences we may have caused by letting PAUP* 4.0 b1 expire without an Updater. To avoid any possibility of repeating this situation, beta 2 will have a much longer expiration period.

Thanks again for your patience,

Jim Wilgenbusch
paup-support

8Mar99

PAUP* 4.0 beta 2 is not yet complete. Dave is very close now and he hopes to have it finished by the end of this week. I have set up a web site where anyone may subscribe themselves to an email list to get the lastest information regarding PAUP* 4.0. Once beta 2 is ready we will post a message to this list. The paupinfo list is one-way e-mail list, meaning that messages will only be sent from paup-support to you.

Jim Wilgenbusch
paup-support

19Feb99

Unfortunately I have once again miscalculated the amount of time it would take to get the second beta version ready. As many of you already know, 4.0b1a will expire at midnight Saturday Feb. 20. I have a travel commitment tomorrow, so the expiration will happen before a new version is ready.

I am close enough to having the new version ready that I really don't want to spend the time that it would take to prepare another Updater extending the life of the first beta for yet another go-round. (This takes hours because of the multiple Macintosh and DOS/Windows versions, creation of the update package, updates to the web page, etc.)

So the new plan is as follows. I will try to finish the new version by Tuesday. If I fail, we will make an Updater available to change the expiration date on the first beta. This means that the program will "officially" be expired on Sunday and Monday.

If this causes a problem for you, remember that there is no self-destruction mechanism on the commercial beta versions-- you can fool the program by changing the date on your computer. Also, the program only checks the date when it is first started, so runs started before Sunday will continue to run until you quit it (e.g., you could start it on Friday and just leave it running in the background until next week).

Once again, I'm sorry for the inconvenience this creates, but I hope you will understand that I've been working extremely hard to improve the program, and I think you will be amazed with the improved searching times if you are working with large data sets. I hope you will also realize that it was pressure from users that led to the release of the beta version before the final release was completed, and that we now spend a lot time supporting hundreds of users that would better be spent finishing the program and manual (i.e., we're doing the best we can--please just bear with us a little while longer). You will hear from me again early next week.

Dave Swofford

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