rsq - a program to facilitate the analysis linkage disequilibrium distance as a function of distance between SNPs
SYNOPSIS
rsq -i <infile>
[options]
DESCRIPTION
rsq calculates several measures of LD (r^2,D, and D'), and outputs them along with the distance between the SNPs. The output file can be processed using another program, such as R (http://www.r-project.org) to make a plot of LD vs. distance. Note that this programs assumes that there is not outgroup present in the data
OPTIONS
rsq accepts the following options:
-i <infile>
specify a file containing aligned sequences in FASTA format to analyze
-h <infile>
specify and outfile in spreadsheet format to analyze. The format of the spreadsheet is:
nseqs nsites
outgroup chars
name chars
EXAMPLE:
2 2
N N
seq1 A A
seq2 T G
In this case, the N's specify that the outgroup was not typed.
-c <mincount>
to be counted in a comparison, a variant at a site must be present greater than mincount times
-t <nperms>
perform a permutation test of the correlation of distance and disequilibrium. <nperms> is the number of times to permute the positions vector