## This site is no longer maintained and has been left for archival purposes

## Text and links may be out of date

Introduction | Downloading | Installation | Usage | back to Evolution at Edinburgh

This is the homepage for a *Mathematica* package for
the analysis of deterministic multilocus population genetic models.
The package was written by
Nick Barton and is described in the paper

- Kirkpatrick, M., T. Johnson and N.H. Barton (2002) General Models of
Multilocus Evolution
*Genetics***162**:1727-1750 (on line)

To use the package you need *Mathematica*, which can be purchased
from Wolfram Research. The packages
have been written for *Mathematica* 4.0 but should also work with
version 3.0, see
here for compatibility information.

The multilocus package has been tested on Macintosh and Linux platforms, and should work on a Windows platform.

The packages are currently at **version 1.02**.

The multilocus package is in fact one of a larger set of *Mathematica*
packages, which are useful in other areas of population genetics and also
contain some utilities to assist in manuscript preparation. An overview of
the packages is here.

**Warning! Even though they are compressed,
the packages are quite large and may take some time to download.**

To download the packages, click on the link appropriate for your operating system or available decompression software.

- Applications.sit a stuffed archive for Macintosh (7.9Mb).
- Applications.tar.gz a tarred and zipped archive for Unix/Linux (3.8Mb).
- Applications.zip a zipped archive for Windows (4.2Mb).

**Warning!
Installing the packages may overwrite
other files that you have previously added to your Mathematica
distribution. If you are at all unsure whether to proceed, you should
consult your local user support.**

To install the packages, you must uncompress the file you have downloaded and then put the uncompressed files in the correct location. The way to do this depends on your operating system.

- Uncompress the StuffIt archive by double-clicking on the icon for the
file you have just downloaded, which should be entitled
`Applications.sit`

. This should automatically uncompress the packages, and a folder called`Applications`

will appear. Some web browsers may perform this step automatically. If you are unable to uncompress the Stuffit archive, you may have to download StuffIt Expander from Aladdin Systems first. - Drag the
`Applications`

folder into the`AddOns`

folder inside the*Mathematica*folder, which is probably something like`Macintosh HD:Applications:Mathematica 4.0 Files:AddOns`

.

- Uncompress the StuffIt archive by double-clicking on the icon for the
file you have just downloaded, which should be entitled
`Applications.sit`

. This should automatically uncompress the packages, and a folder called`Applications`

will appear. Some web browsers may perform this step automatically. If you are unable to uncompress the Stuffit archive, you may have to download StuffIt Expander from Aladdin Systems first. - Find the
*Mathematica*application, which will probably be in the Applications folder - Hold down the Control key, then click and hold on the Mathematica icon. Choose "Show Package Contents" from the pop-up menu that appears
- A new Finder window will open. The AddOns folder is here, but there may already be an Applications folder within it (there is in
*Mathematica*4.1). Drag the contents of the multilocus folder to the AddOns/Applications folder

Depending on how *Mathematica* is installed on your system, you may
need to be root or superuser to install the packages. The exact installation
procedure will vary from system to system. The following instructions
will work on a Linux/GNU system if you have put the downloaded file in
your home directory (your username is fred), so that it is
`~fred/Applications.tar.gz`

, and if
*Mathematica* is installed in `/usr/local/mathematica`

.

`$ gunzip ~fred/Applications.tar.gz`

`$ cd /usr/local/mathematica/AddOns`

`$ su root`

- (type your root password)
`# tar -xf ~fred/Applications.tar`

`# exit`

`$`

If you have difficulty adapting the above procedure to your system, consult your local user support.

- Start the application
**WinZip**(you can download this from www.winzip.com) - In
**WinZip**, choose**Open ...** - Select the file
`Applications.zip`

from wherever you downloaded it to - In
**WinZip**, choose**Extract ...** - Set the
**Extract to**setting to the path of your*Mathematica*`Addons`

folder/directory, which is probably something like`C:\Program Files\Wolfram Research\Mathematica\4.0\Addons`

- Make sure that
**All files**is selected - Make sure that
**Use folder names**is selected - Press the
**Extract**button

The documentation for the packages is provided in the form of *Mathematica* help files. In the
*Mathematica* the front end, select `Rebuild Help Index`

from the `Help`

menu.
(You may need to quit and restart *Mathematica* first.) After the help indexes have been rebuilt
(which may take some time) the documentation for the package can be browsed in the same way as for other
*Mathematica* help. Specifically, click on the `Add-ons`

button in the Help Browser, and
select `Multilocus genetics`

in the leftmost column.

This page is maintained by Toby Johnson and was last modified on the 26th September 2002.

## This site is no longer maintained and has been left for archival purposes

## Text and links may be out of date