PAUP* Test Version Downloads

PAUP* test-version downloads

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Status of PAUP*:

PAUP* is undergoing rapid changes, and will soon be available as a a free, open-source command-line version and a quasi-commercial program with a full GUI interface for Macintosh OSX and Microsoft Windows. 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 report any problems you encounter with this version, no matter how minor (info@phylosolutions.com).

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 you are running Vista, I highly recommend that you update to at least Windows 7.) 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 paup4a157_osx_leopard.

Release notes

PAUP* test-version release notes

Version 4.0a157 (current)

This version one potentially serious bug as well as some other minor bug fixes and small changes.

The feature set for the official release version is now nearly complete (although some new features need to be documented). Unless major problems are found with this version, the official launch of the next major release (5.0) will occur sometime in Fall 2017. Please report any problems you encounter with this version, no matter how minor (dave@phylosolutions.com).

Bugs fixed:

Other changes:

Version 4.0a156

This version corrects a couple of additional issues. (MrModelTest users: Also read the item under Changes for version 4.0a155.)

Bugs fixed:

Version 4.0a155

This version corrects a minor issue with the previous release and adds one simple feature. The feature set for the official release version is now nearly complete (although some new features need to be documented). Unless major problems are found with this version, the official launch of the next major release (5.0) will occur sometime in Fall 2017. Please report any problems you encounter with this version, no matter how minor (dave@phylosolutions.com).

Changes:

Version 4.0a154

This version fixes bugs that caused the previous version to crash with some data files and commands. See the notes for 4.0a153 for other recent changes. The feature set for the official release version is now nearly complete (although some new features need to be documented). Unless major problems are found with this version, the official launch of the next major release (5.0) will occur sometime in Fall 2017. Please report any problems you encounter with this version, no matter how minor (info@phylosolutions.com).

Bugs fixed:

Other changes:

Version 4.0a153

This update adds few new features, but a great deal has changed under the hood to improve reliability, memory usage, and correctness. See the notes below for more information. The feature set for the official release version is now nearly complete (although some new features need to be documented). Unless major problems are found with this version, the official launch of the next major release (5.0) will occur sometime in Fall 2017. Please report any problems you encounter with this version, no matter how minor (info@phylosolutions.com).

Bugs fixed:

Other changes:

Version 4.0a152

This version fixes several bugs that were introduced at 4.0a151, plus a couple of old ones.

Bugs fixed:

Other changes:

Version 4.0a151

This version fixes a few bugs but most of the changes are "under the hood." I will be rolling out several new features early in 2017, but they are still too incomplete and/or buggy to open up for general use at this time.

Bugs fixed:

Other changes:

Version 4.0a150

This release is mainly to fix an SVDQuartets bug that was inadvertently introduced in the previous version.

Bugs fixed:

Other changes:

Version 4.0a149

Important notes regarding SVDQuartets:

The SVDQuartets method is very new and we are still learning things about how to implement it well. Please read the following list of changes carefully and re-run any analyses that might have been affected.

Other bugs fixed:

Other changes:

Version 4.0a148

This version was not released, and changes since 4.0a147 are described above.

Version 4.0a147

This is primarily a bug-fix release, but significant progress has been made on new features that will be opened up in a future version.

SVDQuartets users please read!

An important change has been made to the quartet assembly phase of the SVDQuartets method. Even though the Reaz et al. "QFM" algorithm was performing well with most data sets, it obtained very poor solutions with some larger data sets. The problem was traced to the initial partitioning for each "divide" stop of the divide-and-conquer algorithm. A new strategy was implemented for this partitioning, replacing the corresponding component of QFM. With this new method, QFM performs much better, typically running more quickly than previously and often finding better solutions than other competing algorithms. Because of these changes, it is strongly recommended that any previous analyses be re-run using this new version to confirm that they were not adversely affected by the deficiencies of the previous algorithm.

Bugs fixed:

Other changes:

Version 4.0a146

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: