Bioinformatics: SNPLINK

Project Coordinators: E Webb & RS Houlston

SNPLINK: Multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.

There are 8 files which have been zipped by WinZip 8.0:

  • example1.in
  • example2.in
  • example-chr1.dat
  • example-chr1.pre
  • Installation and user guide.doc
  • snplink.pl
  • snplinkfunctions.pm
  • snplinkfunctionspar.pm
SNPLINK carries out both parametric and nonparametric linkage analysis. The software package Merlin is required for both types of analysis, while the software package Allegro is required for parametric analysis. The R statistical software is required to produce the graphical outputs and Perl is required to run the scripts. All required software is freely available (see links below).

Merlin (Abecasis,G.R., Cherny,S.S., Cookson,W.O. and Cardon,L.R. (2002) Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. 

Nat. Genet., 30, 97-101).

Allegro (Gudbjartsson,D.F., Jonasson,K., Frigge,M.L. and Kong,A. (2004) Allegro, a new computer program for multipoint linkage analysis. 
Nat. Genet., 25, 12-13)

The R Project for Statistical Computing

Download the Latest Version of Perl

Reference: Webb et al. (2005) SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. Bioinformatics.

Search for low penetrance alleles for colorectal cancer through a scan of nsSNPs in 2,575 cases and 2,707 controls.

Project Coordinators: E Webb & RS Houlston