FREE parsimony programs…
The self-extracting file included in this page, pars-win.exe, contains FREE copies of several parsimony programs by P. Goloboff, as well as complete documentation. The programs contained in the package are Pee-Wee, X-Piwe, NONA, PHAST, SPA, and SLF-WT.
Note that these programs (including, as of Nov. 2006, also SLF-WT) have been superseded in almost every aspect by TNT (a joint project by P. Goloboff, James S. Farris, and Kevin C. Nixon). TNT is faster, more powerful, and more user-friendly than all the programs contained here. As of late 2007, TNT became freely available (subsidized by the Willi Hennig Society). The programs in this page are made available mostly for documentation purposes.
There are some pages up in the web with info or user-friendly manuals for Nona (Jerry Miller's and Diana Lipscomb's are two of those).
The most commonly used, of the programs included here, is Nona (Goloboff, 1993). You can also find Linux and Mac OSX versions of Nona, in tarred form. These files include only the binary file, and basic documentation. The Linux and Mac versions have not been carefully tested, so they may have minor bugs or glitches.
How to install the programs under Windows
Download the file pars-win.exe to a directory of its own in your hard disk, and then double-click on the icon of the program. This will extract all the files. NONA is a program for parsimony analysis for additive/nonadditive characters. Pee-Wee implements the weighting method published in Goloboff, 1993 (Cladistics 9:83-91); XPee-Wee does the same, but using floating point precision (so that fit calculations are "exact," as in PAUP*). SPA and PHAST are two programs for Sankoff parsimony; SPA may have every character with any type of transformation cost, while PHAST analyzes data where all sankovian characters have the same, symmetrical costs. The general interface and most commands are identical for all the programs.
The files '*.doc' and '*.dat' are documentation and example data files, respectively. The '*.doc' files are used also for on-line help by the respective programs; do not alter them. The '*.run' files are files that contain instructions for specific tasks; their use and syntax is explained in the file 'programs.doc' (for advanced users only).
The programs contained in the pars-win.exe package must be processed with 'wconvert' to register them to a specific user. If the program is not registered, it will ask the user to press a (randomly chosen) key after execution of each command.
The passwords required to convert the programs are:
Note case!! First argument for wconvert must be the name of the program, second must be the password, and the rest is read as the user name. Thus, to register Winona, for example, to the name of "Paquito Poca Cosa" you need to open a DOS window, go to the directory where you have placed the programs, and type:
wconvert winona yatasto Paquito Poca Cosa < enter>
Three more programs, FQ.EXE, SCG.EXE, and CONS.EXE, are added to the package. These are three simple, free, self-explanatory programs. They calculate majority rule consensus trees (FQ), a special type of majority rule consensus tree (the G-C method of Goloboff et al., 2003) which provides a better measure of support for jacknifing/bootstrapping (GC), and the double consensus method (CONS, which allows for quick estimations of consensus trees). FQ/SCG can be directly used on files created by the instructions contained in the files jak.run, and CONS by the instructions in cons.run.