Estimate linkage disequilibrium between unphased loci
The software in this directory implements a method for estimating linkage disequilibrium, which is described in the following publication.
@Article{Rogers:G-182-839,
author = {Rogers, Alan R. and Chad Huff},
title = {Linkage Disequilibrium between Loci of Unknown Phase},
journal = {Genetics},
year = 2009,
volume = 182,
number = 3,
pages = {839--844},
month = {July},
}
FILE DESCRIPTION
estimate_ld.py Implements various estimators of LD. If you write your
own Python program, import this as a package.
myexcept.py Defines exceptions used by the other programs.
tst_r.py Tests the functions in estimate_ld.py.
covld.py Reads a data file and estimates LD using the Rogers-Huff
method and (optionally) the Excoffier-Slatkin method.
For usage info, type "python covld.py -h".
covld-dat.txt Sample input file for covld.py. The input format is
described in the header of this file.
This software is all in the public domain.
Alan R. Rogers