PAUP* Test Version Downloads

PAUP* test-version downloads

Status of PAUP*:

PAUP* is undergoing rapid changes, and will soon be available as a quasi-commercial program with a full GUI interface for both Macintosh OSX and Microsoft Windows and a free, open-source command-line version. While final development and testing is underway, we are making these test versions available as a free download. They will expire every few months, and you will need to update when this happens. Versions can updated using either an auto-updating system (GUI version) or just returning to the download site (both versions).

Once we have decided to make an official release of the GUI version, it will no longer be freely downloadable, and test versions will no longer auto-update. At that time, however, the command-line version will become non-expiring, free, and open source.

You are welcome to use these versions in the meantime, however I cannot promise any support or guarantee correctness or accuracy. Use at your own risk. Please send any bug reports to me directly (david.swofford@duke.edu)

Macintosh OS X Leopard (GUI version; universal binaries):

Note: After extracting the downloaded file (if necessary), you may need to right-click the icon and choose Open the first time (to get around the warning that the application is from an unknown developer).

Windows GUI version:

This version now officially requires Windows 7 (either 32- or 64-bit), but probably runs under Vista as well. (If sufficient need could be demonstrated, I could probably supply a version for Windows XP, but I am hoping not to do this.) There may be a few as-yet-undiscovered glitches in the dialog boxes, so please report these if you encounter them.

Command-line binaries:

Note: After gunzip'ing the downloaded file (if necessary), you may need to make it executable using a command like chmod a+x paup4a146_osx_leopard.

Release notes

PAUP* test-version release notes

Version 4.0a146 (current)

Changes:

Bugs fixed:

Version 4.0a145

This version addresses major problems with the previous version released about 3 weeks ago (I was rushing to get an update finished before a workshop, and my testing was inadequate after making a complicated under-the-hood change intended to reduce memory usage). The problems were mostly, but not entirely, associated with the deletion of taxa (and there may well have been problems in addition to those reported below). There may still be a few related issues, but I wanted to get an update out as soon as possible.

In adition, there was a problem with the ML settings dialog interface that caused use of the "previous" buttons associated with model parameter estimates to have no effect (model parameters were still subsequently estimated by ML when the interface claimed to have set them to fixed values). Searches were then excruciatingly slow, as model parameters were being estimated for each tree evaluated in a search, which I never recommend doing.

Finally, the bug with the partition homogeneity (=ILD) test was not completely fixed as reported in 4.0a144. Results were valid only if (1) characters in each partition subset were contiguous and (2) there were exactly two subsets in the partition. (Unfortunately, these conditions were both true for the data set that caused me to recheck the test, and I didn't test other cases.) I am satisfied that the test is now working correctly when characters in each subset are not contiguous (e.g., codon positions) as well as when more than two subsets are present.

Changes:

Bugs fixed:

Version 4.0a144

New features:

Serious bug fixed:

Other changes:

Bugs fixed:

Version 4.0a143:

Not released.

Version 4.0a142:

This update fixes several bugs affecting likelihood, distance, and SVDQuartets analyses. In addition, a console (command-line) version is also now installed along with the Windows GUI version (after installation, you should be able to invoke this console version by typing "paup" in a command-prompt window).

Changes:

Bugs fixed:

Version 4.0a141:

This release addresses numerical problems in the Windows version that sometimes cause premature termination of maximum-likelihood optimizations. Windows users should update to this version; the most recent Mac/Linux release remains 4.0a140.

Bugs fixed:

Version 4.0a140:

This release addresses a memory corruption issue that primarily affects the Windows version. All Windows users should update if they are doing maximum likelihood analyses. Mac users should update as well unless it is inconvenient for some reason.

Bugs fixed:

Version 4.0a139:

This is yet another quick bug-fix release to fix a stupid mistake I made while rushing to get an update ready for a workshop. The bug was serious; please apply the update. Also check the release notes for previous versions if you have not already done so..

Bugs fixed:

Version 4.0a138:

This is a quick bug-fix release to address several issues with maximum likelihood in verison 4.0a137. Please see the release notes for that version as well.

Bugs fixed:

Version 4.0a137:

New features:

Other changes:

Important note:

Maximum-likelihood bootstrapping has apparently been broken for over a year without me (or apparently anyone else) noticing it. The problem was so severe that it is extremely unlikely that you would have accepted the results as valid (in fact you probably would not have even been able to get a run to finish). However, if you somehow managed to perform an ML bootstrap analysis with any version between 4.0a130 and 4.0a136, you need to repeat the analysis.

Bugs fixed:

Version 4.0a136:

New features:

Other changes:

Bugs fixed:

Version 4.0a135:

This version was not distributed. See release notes for 4.0a136.

Version 4.0a134:

New feature:

Other changes:

Bugs fixed:

Version 4.0a133:

Changes:

Bugs fixed:

Version 4.0a132:

This version was not distributed.

Version 4.0a131:

Version 4.0a130:

Important note:

After a bit of soul-searching, I have decided to change the default multithreading setting to be a single thread. Previously, I queried the system for the number of cores available and defaulted to one thread per core. The problem with this method is that many machines now have a large number of cores, and using this many threads degrades rather than enhances performance. Also, on a machine running multiple long jobs, better system performance is obtained by not having all of these jobs compete for the same set of cores. This is is especially relevant for jobs running on HPC clusters using the Sun Grid Engine for scheduling--the operating system will happily report that (say) 16 cores are available even though there are already 15 other jobs running on a node.

So now, if you want to use multithreading for maximum likelihood calculations, you must explicity specify lset nthreads=n; (where n > 1) before beginning a likelihood analysis (or use the equivalent setting from the "Optimization" pane of the "Likelihood Settings" dialog box). You will probably want to do some experimentation to determine the best value for nthreads--two to four may be better than one, but depending on the size of the data, requesting too many threads will be detrimental. You can also use lset nthreads=auto; to obtain the old behavior of using one thread per core.

New features:

Changes:

Bug fixes:

Version 4.0a129:

New features:

Bug fixes:

Version 4.0a128:

Yes, I know. The previous version (4.0a126) was a disaster. I decided to add support for multiple Characters blocks in Nexus input files in order to support (e.g.) Mesquite-generated files that were causing PAUP* to crash. This turned into a big mess and I had to rush a version out for the European Molecular Evolution Workshop, Several new bugs were introduced during this period. Unfortunately, I then I got hopelessly busy on non-PAUP-related projects and couldn't work on the program for a while.

Anyway, the problems fixed in this release include: With regard to multiple Characters blocks, note that TITLE and LINK blocks created by Mesquite are currently ignored. If you use multiple Characters blocks, they must conform to a preceding Taxa block (i.e., the same taxa, in the same order). Eventually I may try to improve support for Mesquite's extensions to the Nexus format, but this is a start.

This version also provides a few additional fixes and improvements:

Version 4.0a127:

This build was not generally released..

Version 4.0a126:

Version 4.0a125:

Version 4.0a124:

Version 4.0a123: