Back to SimWalk2 Overview

SimWalk2: Additional Resources and References

Additional Resources:

The program Mega2, used to convert LINKAGE-format locus, pedigree, map and penetrance files to the MENDEL-format used by SimWalk2, is available from <register>. Mega2 can also be used to coordinate the use of precomputed NPL scores by SimWalk2.

Version 3.35 of the general pedigree analysis package MENDEL, used by SimWalk2 to generate location scores, may be obtained from Dr. Kenneth Lange at the addresses below. Note that SimWalk2 uses version 3.35 of MENDEL, not version 4 or later.

e-mail:	<mailto:klange@ucla.edu>
WWW:	<http://www.biomath.medsch.ucla.edu/faculty/klange/software.html>
mail:	Kenneth Lange Department of Human Genetics David Geffen School of Medicine at UCLA Los Angeles, CA 90095-7088 USA
tel:	+1-310-206-8076.

The Windows program Cyrillic, used to draw out overall haplotype vectors, may be found at <http://www.cyrillicsoftware.com>.

The MacOS program Pedigree/Draw, used to draw out overall haplotype vectors, may be obtained from The Southwest Foundation for Biomedical Research at <http://www.sfbr.org/sfbr/public/software/software.html>.

Other haplotype drawing programs designed to work with SimWalk2 include HaploPainter <http://sourceforge.net/projects/haplopainter> and Madeline <http://eyegene.ophthy.med.umich.edu/madeline>.

References:

If you publish results generated by SimWalk2, then please cite the Sobel and Lange (1996) article from the following reference list.

Lange E and Lange K (2004)
Powerful allele-sharing statistics for nonparametric linkage analysis
Human Heredity 57:49-58

Sobel E, Papp JC and Lange K (2002)
Detection and integration of genotyping errors in statistical genetics
American Journal of Human Genetics 70:496-508.

Sobel E, Sengul H and Weeks DE (2001)
Multipoint estimation of identity-by-descent probabilities
at arbitrary positions among marker loci on general pedigrees
Human Heredity 52:121-131

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.

Sobel E, Lange K, O'Connell JR and Weeks DE (1995)
Haplotyping algorithms.
In "Genetic Mapping and DNA Sequencing" Speed T & Waterman M, eds.
IMA Volumes in Mathematics and its Applications vol.81 pp.89-110.

Weeks DE, Sobel E, O'Connell JR and Lange K (1995)
Computer programs for multilocus haplotyping of general pedigrees
American Journal of Human Genetics 56:1506-1507.

Whittemore AS and Halpern J (1994)
A class of tests for linkage using affected pedigree members
Biometrics 50:118-127.

Sobel E and Lange K (1993)
Metropolis sampling in pedigree analysis
Statistical Methods in Medical Research 2:263-282.

Lange K and Sobel E (1991)
A random walk method for computing genetic location scores
American Journal of Human Genetics 49:1320-1334.

Lange K and Matthysse S (1989)
Simulation of pedigree genotypes by random walks
American Journal of Human Genetics 45:959-970.

Lange K, Weeks DE and Boehnke M (1988)
Programs for pedigree analysis: MENDEL, FISHER and dGENE
Genetic Epidemiology 5:471-472.

Lange K and Goradia T (1987)
An algorithm for automatic genotype elimination
American Journal of Human Genetics 40:250-256.