Introduction

The program TreeLD implements a statistical method for analyzing genotype data in association/linkage disequilibrium studies. It can be applied both for fine-mapping the location of a disease mutation and for performing tests for association. The underlying method is based on making inferences about the presence and location of a disease mutation by reconstructing the ancestry of a set of sequences. The software is designed for SNP-data and can accommodate both case-control data and chromosomes from a TDT test. Our package is named TreeLD, to reflect the emphasis on estimating the ancestral trees that relate the sampled chromosomes at different positions across a region of interest. The computational algorithm underlying TreeLD 1.0 is named LATAG. LATAG and the philosophy behind our method are described in Zöllner and Pritchard (2005).

The Program produces two kinds of results:

• p-values for significance testing for the presence of disease mutation(s) in a region
• estimates and credible regions for the location of a disease mutation

In addition, the program outputs additional information such as the estimated trees relating sampled chromosomes. These can be used to help visualize the subset of the data containing the where the signal.

This document describes the use of the program TreeLD, which is free and comes with no warranty whatsoever. Downloads for the software will be made available via

$$http://pritch.bsd.uchicago.edu/software.html$$

This webpage provides a version of the program for Windows NT, for the Unix Solaris and for Linux. Please send bug reports and requests for new features to Sebastian Zöllner at szoellne@genetics.bsd.uchicago.edu. We ask downloaders to complete the software registration form on the web page.