This site is no longer maintained and has been left for archival purposes

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Multilocus Package

Multilocus Package

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

Introduction

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

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.

Downloading the packages

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.

Installing the packages

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.

Macintosh (OS 9 or earlier)

  1. 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.
  2. 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.

Macintosh (OS X)

  1. 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.
  2. Find the Mathematica application, which will probably be in the Applications folder
  3. Hold down the Control key, then click and hold on the Mathematica icon. Choose "Show Package Contents" from the pop-up menu that appears
  4. 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

Unix/Linux

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.

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

Windows

  1. Start the application WinZip (you can download this from www.winzip.com)
  2. In WinZip, choose Open ...
  3. Select the file Applications.zip from wherever you downloaded it to
  4. In WinZip, choose Extract ...
  5. 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
  6. Make sure that All files is selected
  7. Make sure that Use folder names is selected
  8. Press the Extract button

Using the packages

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