PAUP* Test Version Downloads

PAUP* test-version downloads

Status of PAUP*:

NOTE: Mac and Windows GUI versions have been updated to (unexpired) 4.0a139. Linux and command-line versions are still underway.

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 (available from Sinauer Associates), 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 it 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 (

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 has been tested on Windows XP and Windows 7 (both 32- and 64-bit). 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 paup4a139_osx_leopard.

Release notes

Version 4.0a139 (current):

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:


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:


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:

Version 4.0a122:

Version 4.0a121:

Version 4.0a119/4.0a120:

Version 4.0a120 just extends the expiration date to 1 Feb 2012 to avoid possible end-of-semester unpleasantness for those using it in courses (a119 and a120 are identical otherwise).

Version 4.0a118:

Note: There were serious problems with the Kishino-Hasegawa test in versions 4.0a112-4.0a114 (introduced accidentally while implementing the AU test). Please repeat any analyses involving KH tests performed using these versions before publication!

Version 4.0a117:

Version 4.0a116:

Version 4.0a115:

Version 4.0a114:

Version 4.0a113:

Version 4.0a112:

Version 4.0a111 notes

A few bug fixes, plus Shimodaira's AU test availability.

Specific changes since 4.0d110 include:

Version 4.0a110 notes

Once again, mostly just bug fixes, but stay tuned.

Specific changes since 4.0d109 include: