Genetic Linkage Analysis Project

SUPERLINK
version 1.7

Superlink Online SNP

The Superlink online version is the recommended way to use Superlink. This version is easy to use, provides many features not available in the standalone version and performs massively parallel computations using thousands of CPUs.

Last Updated - November 11, 2008

Background

Genetic linkage analysis is a statistical method that is used to associate functionality of genes to their location on chromosomes. The main idea is that markers which are found in vicinity on the chromosome have a tendency to stick together when passed on to offsprings. Thus, if some disease is often passed to offsprings along with specific markers, then it can be concluded that the gene(s) which are responsible for the disease are located close on the chromosome to these markers.
Superlink is a computer program that performs exact genetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs Linkage, Fastlink v4.1, Tlinkage, Vitesse v2.0, and Genehunter v2.1. Superlink can run larger files than previous programs.

Features of Superlink

Analysis of general pedigrees (many individuals, inbreeding loops, many markers, etc.).
Analysis of two-locus traits.
Analysis of autosomal or sex-linked traits.
Maximum-likelihood Haplotyping analysis.
Analysis of complex traits.

Modifications introduced into Version 1.7

Efficient implementation of Lander-Green algorithm (as in Genehunter) capable of analyzing very large (tens of thousands) number of markers by using the hard drive.
Improved algorithm for deciding when to run Superlink-based algorithm and when to run Genehunter-based algorithm.
Fixed several bugs which led to incorrect compution of two-loci disease model.

Experimental Results

Version 1.7 has been introduced to enable the analysis of small-to-moderate sized pedigrees with potentially very large number of markers .

Experimental results of Version 1.7 (updated Nov 11, 2008).

Executables (Version 1.7)

You can also use Superlink without downloading it via a simple web interface Superlink-online which is faster due to the use of thousands of computers worldwide.

Format of Input Files

Superlink's input format is almost the same as that of Linkage/Fastlink (see Linkage User's Guide) except for Superlink's additional options. The input format for two-loci traits is identical to the one used by Tlinkage. The two additional program options of Superlink require a slightly modified input format which is explained in more detail in Format of Locus file. Some options of Linkage/Fastlink have not been implemented, as detailed in Format of Locus file.

There are two input files. One file describes the loci being analyzed (locus file). The second file holds information regarding the pedigree (pedigree file).

Operating Instructions

Put locus and pedigree files in the working directory.
Type "superlink <locus-file-name> <pedigree-file-name>" and press <Enter>.
The default name for the locus file is datafile.dat. The default name for the pedigree file is pedfile.dat.
If you are using the default names for the input files, then it is enough to type "superlink".
To test the program, download datafile.dat and pedfile.dat and type "superlink" with no arguments.

The result is LOD_SCORE = -0.402989.

The data files of our experiments (Experimental Results v1.0, Experimental Results v1.2, Experimental results of Version 1.4 or Experimental results of Version 1.5) can also be used to test Superlink on your computer with your favorite size pedigree.
Give it a try!

Previous Versions

Publication References

"Exact Genetic Linkage Computations for General Pedigrees." Fishelson M. and Geiger D. Bioinformatics, 2002; 18 Suppl. 1: S189-S198.
"Optimizing Exact Genetic Linkage Computations." Fishelson M. and Geiger D. Journal of Computational Biology, 2004; 11(2-3): 263-75.
"Maximum Likelihood Haplotyping for General Pedigrees." Fishelson M., Dovgolevsky N. and Geiger D. Human Heredity, 2005; 59:41-60.
"Narated Power Point presentation of the principles behind Superlink" UAI2003, 2003. Beware 107MB, downloading can take some time.
"A Bayesian LOD Score for Linkage Analysis of Complex Diseases." Fishelson M., Rusakov D. and Geiger D. Technical Report CS-2004-12.
Newspaper article about Superlink (in Hebrew). Appeard in NFC (July, 2003).

Helpdesk

For comments and bug reports please send email to superlink-online.
You can use Superlink also via a simple web interface without downloading it at Superlink-online.

Written by Ma'ayan Fishelson.