Linkage Disequilibrium Analyzer (1.0)

LDA is a Java program for analyzing the pairwise linkage disequilibrium, developed by Keyue Ding, Kaixin zhou, Fuchu He and Yan Shen. This program is free for academic use only and can be downloaded here. The LDA is required that the Java 2 Runtime Environment, version 1.4.0 or later be installed to run the program properly.

Reference:
Keyue Ding, Kaixin Zhou, Fuchu He, and Yan Shen. (2003). LDA - A java-based linkage disequilibrium analyzer. Bioinformatics. 19: 2147-2148.

Please choose the version that you want to use.

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Windows Release 1.0 (Download 1.92MB | with JVM Download 11.8Mb)

 Instruction:

After downloading, double-click install.exe

Notes:

If you do not have a Java virtual machine installed, be sure to download the Java 2 Runtime Environment from Sun's Java web site.

Linux Relase 1.0 (Download 2.03MB | with JVM Download 34.5MB)

Instruction:

After downloading open a shell and, cd to the directory where you downloaded the install.bin

At the prompt type: sh ./install.bin

Notes:

You need to install a Java 1.1.8 (or later) virtual machine. You can download one from Sun's Java web site.

Mac OS X Release 1.0 (Download 1.64MB)

 Instruction:

After downloading, double-click install

Notes:

Requires Mac OS X 10.2 or later

Java 1.4.1 Developer Preview 8 and Tools Update  has been posted to the "Download Software" area of the ADC Member Site.

The compressed installer should be recognized by Stuffit Expander and should automatically be expanded after downloading. If it is not expanded, you can expand it manually using StuffIt Expander 6.0 or later.

If you have any problems launching the installer once it has been expanded, make sure that the compressed installer was expanded using Stuffit Expander. If you continue to have problems, please contact technical support.

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There is a tutorial about the program within the help system of this release.

If you find any problem about using this program, please contact: Keyue Dingor Kaixin Zhou.

Last modified on February 5th, 2004

Update information (Feb 5th, 2004)

1, correct the bugs in the degrees of freedom in HWE chi-square test. (Thanks for Prof. Nelson LS Tang for bug report; Department of Chemical Pathology, The Chinese University of Hong Kong).

Update information (Feb 25th, 2003)

1, correct the bugs in calculating allele frequency, taking into account missing data;

2, correct the bugs for better demonstration of few SNPs loci of graphical output;

3, add the chi-square test for LD test and HWE test;

4, give more tutorial on guiding the user to use LDA in help system;

5, correct some spelling error in the output;

The old version is accessible on http://www.chgb.org.cn/lda_beta/lda.htm

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