Known Problems -- PAUP* 4.0
Beta 10

Below is a Listing of known bugs and other problems that are at some stage of repair. The list of bugs/problems is broken into the following sections:

  1. General (i.e., all versions)
  2. Macintosh version
  3. Portable-interface (e.g., UN*X and DOS)
  4. Windows-interface (95/98/NT)

General problems:

  • The option name "Method" under the "RootTrees" command was changed to "RootMethod" in Beta 10. Beta 10 and greater will no longer recognize the option name "Method"; use "RootMethod" instead.
  • Proportion of invariable sites and gamma distributed rates are both ignored in a distance-based bootstrap analysis.
  • The steepest descent options (steepest) under the hsearch command is broken when run in conjunction with the random addition sequence option. Do not use the steepest option with random addition sequence until this bug is fixed.
  • There is a bug in beta 10 that is causing PAUP* to output bogus values for the relative contribution for each rate category to the display buffer. As a workaround the values are correctly written to the scorefile. For example:

lscore 1 /rates=gamma shape=est sitelikes=yes categlikes=yes scorefile=catelikes.out;

  • Heuristic searches using random addition sequence will occasionally save more trees than should be saved.
  • The KH-test is broken when the normal distribution is used as the test distribution. You can work around this problem by using RELL as the test distribution. For example:

lscore 1 2/khtest=rell;

  • Using the "factory" command in batch mode will cause character positions that contain gaps to be omited from likelihood analysis. Factory causes the gapmode option to be set to "newstate" internally. The best way to work around this problem is to omit the factory command from the first paup block in your batch file and set options explicitly.
  • Branch lengths values given under the accelerated transformation character state optimization are incorrect for some tree rootings. Tree scores are correctly calculated, however branch lengths may be exaggerated so that they sum to a value greater than the tree length.
  • Rate matrix parameter estimates are not being save to the likelihood scores file. This will especially cause problems for those using the program Modeltest (by David Posada) because Modeltest uses the score file as its input. A short-term work around for the LScores scorefile/ModelTest problem is to use the longfmt=yes option under the LScores command. For example run the following command before executing the "modelblock" file.

default lscores longfmt=yes;

  • Bootstrap consensus trees are not being saved by the "Savetrees" command or by the equivalent menu option. The easiest way to get arount this problem is to use the "from/to" options under the savetrees command. For example, after running the bootstrap command type:

savetrees from=1 to=1;

  • Running the permutation test PTP will give the message " 'Enforce constraints' option requested but no constraints have been defined". A short-term workaround is to define an arbitrary constraint and then re-execute the data file. For example:

begin paup;
constraint futz = ((1,2)); [added to get ptp test to work]
permute test=ptp;

Macintosh version only:

  • Saving current settings as startup defaults will cause a crash on Macs running System 8.0 and 8.1. The only way to get around this until we release a new update is to upgrade your OS.
  • Running PAUP on systems with Mac OS 7.5.x may give the message that the "AppearanceLib" could not be found. We are going to release another version of PAUP* that will eliminate the requirement for this library. Until this release, you can fix the problem by upgrading your system to Mac OS 7.6 or greater. You could also try downloading and installing the AppearanceLib Extension into your extension folder. The later solution is not guaranteed to work as your system may then ask for the UnicodeConverter.

The AppearanceLib Extension:

Portable-interface (e.g., UN*X and DOS):

  • The portable (Unix) version for Mac OS X failed to execute because the standard Mac OS X system implements an old version of curses (a library used to enable command recall functionality). This problem has already been fixed, however, if you downloaded the beta 10 tar archive yesterday (Mar3) or today you will need to download the current archive.

    Windows-interface versions only:

    • None reported

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