Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. The LINKAGE program suite was an earlier package for genetic linkage analysis. FASTLINK is a signficantly modified and improved version of the main programs of LINKAGE that run much faster sequentially, allow the user to recover gracefully from a crash, and provides new improved documentation.

The SLINK package contains a simluation program slink and backend programs unknown, msim, lsim, isim. SLINK generates random replicates, and msim, lsim, isim analyze the replicates.

SUP is an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with a trait locus. This version of SUP is meant to be used only with version 3.0 or above of FastSLINK (released in March 2010). Using version 3.0 of FastSLINK, there's no upper limit to the number of founders a pedigree may have. Also, by using 'slink -t' instead of 'slink', the trait locus genotypes are now readily available in a new output file, which simplifies the whole simulation set up.

The FastSLINK program is the merger of code from FASTLINK version 2.x to the slink program, by Alejandro Schaffer and Dan Weeks.

FASTLINK homepage at NCBI

The FASTLINK project is directed by Alejandro Schäffer. 

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

There are fastlink, fastslink and sup modules. User can run individual ones or combine modules. The program 'unknown' exists in both fastlink and fastslink and there maybe version difference between them. The last issued module will overwrite previous ones. For example, the 'unknown' in fastSlink will be used if user first run 'module load fastlink' then run 'module load fastslink'.

$ module avail fastlink
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
fastlink/current

$ module load fastlink

$ module list
Currently Loaded Modulefiles:
  1) fastlink/current

$ module unload fastlink

$ module load fastlink/current

$ module show fastlink
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/fastlink/current:

module-whatis    Sets up fastlink 
prepend-path     PATH /usr/local/apps/fastlink/ 

-----------------------------------------------------------------

Sample session

$ module load fastlink
$ mlink
Program MLINK version  5.10 (1-Feb-1991)

FASTLINK version 4.1P (30-Jun-1999)

The program constants are set to the following maxima:
     8  loci in mapping problem (maxlocus)
    25  alleles at a single locus (maxall)
 50000  maximum of censoring array (maxcensor)
 [.....]

$ module load sup
$ sup -p [-pre] <pedfile> -d <datafile> -o <outfile>
 [.....]

$ module load fastslink
$ which unknown
/usr/local/apps/fastslink/3.02/unknown

$ module load fastlink
$ which unknown
/usr/local/apps/fastlink/unknown

Documentation

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html

[Paper 1] [Paper 2] [Paper 3] [Paper 4] [Loops in Fastlink] [Pedigree traversal] [UNKNOWN docs] (PDF)

http://watson.hgen.pitt.edu/docs/SLink.html

/usr/local/apps/fastslink/sup-fastslink-tutorial/