SimWalk2

Online Docs :: Download

SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.

Please let me know if you have any questions about SimWalk2 and in particular if there are any changes or additions that would make this program more useful to you.

Thank you, Eric Sobel

Contact Information:

Eric Sobel

simwalk@genetics.ucla.edu

Citation:

  1. Sobel E and Lange K (1996) Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. American Journal of Human Genetics 58:1323-1337.
  2. Sobel E, Sengul H, Weeks DE (2001) Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees. Human Heredity 52:121-131.
  3. Sobel E, Papp JC, Lange K (2002) Detection and integration of genotyping errors in statistical genetics. American Journal of Human Genetics 70:496-508.

New Features In This Version

SimWalk2 version 2.91

In 2.91 the Kinship Exchange File now includes the simple IBD probabilities; hence the files are now called IBD and Kinship Excahnge Files (IKEF). The Sun executables have been made more robust. The number of loci that SimWalk2snp can analyze is reduced, usually to 768. There is more coordination with Mendel 5.7. Please see the file WhatsNew_291.txt for more information.

In 2.89 the NPL analysis is improved and better coordinated with other programs. Mistyping and Haplotyping output is improved and extended. Run times are automatically extended for very fine maps. A second executable, simwalk2snp, is included for datasets with many biallelic markers. Also, files to export expected allele counts to QTL programs are produced.

In 2.86 the IBD analysis is much faster for the vast majority of pedigrees. Also, files to export kinship coefficients to QTL programs are produced.

In 2.83 a feature is added to greatly speed up the NPL analysis through coordination with the software programs Mega2 and Merlin.

In 2.82 the mistyping analysis is greatly improved. Also, the parametric analysis option now allows for locus heterogeneity in more generality.

If you are still using a version of SimWalk2 older than 2.60, then please consider this a MANDATORY upgrade since the fixes introduced in version 2.60 can significantly effect the p-values of the statistics from the Non-Parametric Linkage analysis!