SNPpattern - identify haplotype blocks from phased genotype data

SNPpattern is the collective name for a suite of Perl scripts. The scripts are essentially designed to
group, count, and compare SNP patterns of various block sizes found in phased genotype data extracted
from a group of individuals. A multiple SNP block model and a pattern similarity score are used as the
two main approaches for studying the SNP patterns. Two suggested applications of SNPpattern are:
examining LD structure (haplotype diversity) within or between groups of individuals, and finding
common (highly conserved) SNP patterns for use in association studies. This document explains how
to install, run, and configure SNPpattern.

1.1 How to get started
There are fundamentally only 4 steps to get started:
1) Download software;
2) Install Perl;
3) Modify configuration files;
4) run Perl scripts.

1.1.1 Download software
A compressed SNPpattern directory containing all relevant files (including Perl scripts and example
configuration files) can be downloaded from the following URL:

For Windows:
http://web4ftp.it.csiro.au/ftp4goo17a/SNPpattern/SNPpattern.zip

For Linux:
http://web4ftp.it.csiro.au/ftp4goo17a/SNPpattern/SNPpattern.tar.gz