There are two main lde programs you can run: genbin.lde.pl and lde++. GENBIN.LDE.PL: This program is a wrapper on a bunch of perl programs. It sits in /usr/local/genome/bin. The helper programs are in /usr/local/ genome/lib/lde. It has an argument of -prettybase. The output files have the same prefix as the prettybase and consist of the following: <prefix>.hap.count.txt <prefix>.lde.stat.exception <prefix>.lde.txt <prefix>.maketable.txt You will have to see Lakshman for a detailed account of what these gilrd contain. The most important file is the .lde.txt file. The results in this file are interpreted as follows: d2 > .1 is significant if chi2 > 3.68. LDE++: This program creates a triangular plot of the .lde.txt file. Accordingly, the argument to this program is -file <prefix>.lde.txt. There are two optional arguments: -unit and -stat. The unit argument makes the picture larger or smaller. If the unit > 20, then the sites are numbered on the top of the plot. It's supposed to be the name of the site, but that doesn't always work. The stat argument lets you choose which statistic it uses to create the plot. The default is d2, but you can also choose either chi or D.