The documentation files are in two forms. One is this web page, which you should download if you are getting the programs, and you should also download its icon graphic. If you want the equivalent material as a text file you can alternatively get simul8.doc.
To run the program on Unix systems, in DOS, or in a Windows MSDOS box, you should simply type simul386 or simul8, which cause the program SIMUL386.EXE or SIMUL8.EXE to be read into the computer's memory and executed.
The program uses a random number generator. It should give you a different result every time it is run.
For the Sun, Linux, IBM, Compaq/DEC Alpha, or DECstation executables just make sure the executable has execute permission (the command is chmod +x simul8.sun, chmod +x simul8.dec, or chmod +x simul8.alpha). That only needs to be done once.
To run them type the name of the program.
The Macintosh version provided here is a variant of a program, PoPG 1.0, written by Mark Wells. That in turn was based on an earlier version of Simul8. It is started by double-clicking on the program icon. It opens a window to set parameter values, then is controlled using the Run and File menus. It has two migration models (stepping-stone and source/sink) that are not found in the other versions of Simul8. There are two executables provided, Simul8PPC and Simul868. The former is for PowerMac systems, the second for older (68k non-PowerMac) systems, although it too can run, somewhat slowly, on PowerMacs. Note that as stored in this ftp area, the executables are files in the MacBinary format.
Download (by clicking on these links):
The Makefile can be used on most Unix workstation to compile the program by simply putting simul8.c and the Makefile into a directory and then typing make. That will tell you what to do (which depends on your workstation). If that does not work, then use one of these:
cc simul8.c -DX -lm -lX11 -o simul8
or if you are on Openwindows on a Sun SPARCstation:
cc simul8.c -DX -lm -lX11 -o simul8 -I/usr/openwin/include -L/usr/openwin/lib -o simul8
The resulting executable (simul8) can display on any X terminal or X-capable workstation.
If you are compiling on a Sun SPARC for use on Suns other than the one on which you are compiling, you might want to add the switch -Bstatic to force the compilation to not use dynamically linked libraries, as these may differ among machines and cause trouble.
The program is written to work on a variety of different systems, with several different graphics displays. When the program starts running it asks you to choose one of the displays. You will probably want to choose the graphics setting, (option number 1).
On DOS or Windows systems the colors of the graph may be hard to read. To change them choose option 0 when the main menu appears. On X-windows systems the window for the gene frequency plots has an irritating tendency to overlap the area where you are supposed to type, and the text window where you are to type may have to be clicked on to make it active too. You will want to resize the main text window and/or move it out of the way. You may have to be careful where your cursor is or which window you have clicked on.
The Macintosh version is based on a program, PopGen 1.0, written by Mark Wells for Doug Schemske of our Botany Department. That in turn was based on earlier versions of Simul8. It has two versions, one for 68k Macs and one for PowerMacs. Although the first will also run on PowerMacs, it is better to run the native PowerMac code, as that runs more quickly. On old Macs that do not have a math coprocessor the program will run very slowly as it is emulating math coprocessor functions, and that emulation is slow.
The programs simulate eight simultaneously evolving populations with you specifying the population size (less than or equal to 10000), the fitnesses of the three genotypes, the mutation rates in both directions (from A to a and from a to A), and the initial gene frequency. They also ask for a migration rate among all the populations, which will make their gene frequencies more similar to each other. Much of the time (but not always!) you will want to set this to zero. In most respects the programs are self-explanatory.
When you run the program a main menu appears showing you the settings of these parameters. In the DOS/Windows and Unix versions you change any of them by typing the digit (0 through 9) that appears on the left side of that line. The program will then ask you for a new value of that parameter. You can reset any or all of them. In the Macintosh and PowerMac versions you edit the values that appear in the menu in the usual Macintosh way.
The program will display a plot of the gene frequencies for that case for each of the populations, plus a dashed curve that shows what the gene frequencies would be in an infinite population. In the DOS/Windows and Unix versions, after showing the proper number of generations the program asks you if you want to specify the number of generations to simulate. If you just press the Enter key at this point you get another run of the same number of generations. If you type in the number "0" it will stop the simulation and return to the main menu. The number of populations in which the allele A has been fixed and the number in which it has been lost are also shown.
In the Mac and PowerMac versions you should use the Run menu to Continue the run, or its Start option to start a new run with the same parameter values, or its New Case option to choose new parameter values for a new run. You can stop by choosing the Quit option from the File menu. In the Mac and PowerMac versions you can also resize the graph by altering the lower-right corner of the graph's window. In the DOS/Windows and Unix versions, you can also type P when asked for the number of generations. This causes the program to write out a file in the Postscript language that plots a graph of the current screen. You will be asked for a file name. After you have finished running the program, you can send that file to a Postscript printer (such as an Apple Laserwriter, but not an HP Laserjet-compatible printer unless it also has the ability to print Postscript). On PCDOS this is done by a command like (if the file name is FOO.PS) COPY FOO.PS PRN:, on workstations you may be able to use the lpr foo.ps command. After writing the file when you type P and specify the file name, the system returns to asking you about the number of generations you want to simulate.
On the Mac and PowerMac version you can choose the Print option from the File menu to print the current graph to your computer's printer. Note that if you have resized the graph, you may find that it prints past the margin of the paper, unless you use Landscape printing.
The program can simulate a wide variety of cases, and you should explore some of these.
Simul8 was written by Joe Felsenstein, Hisashi Horino, Sean Lamont, Bill Alford, and Mark Wells. It is copyrighted to Joe Felsenstein but can be freely copied and run provided no fee is charged for it and provided that the copyright notices are not removed.
|Department of Genetics|
|University of Washington|
|Seattle, WA 98195-5065, USA|
email: joe (at) removethispart.gs.washington.edu