Simwalk

Record added by Jurg Ott (the original Rockefeller list)

SIMWALK/SIMCROSS

SIMCROSS: June 1995; SIMWALK2: 2.91 (December 2004)

programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method.

Eric Sobel (UCLA. email: simwalk@genetics.ucla.edu (in collaboration with Kenneth Lange, Jeffrey O’Connell,, Daniel E. Weeks)

• http://www.genetics.ucla.edu/software/simwalk
• registration page at: http://www.genetics.ucla.edu/software/registration or, http://watson.hgen.pitt.edu/register/

FORTRAN77

UNIX(SunOS/Solaris)

• Weeks, Sobel, O’Connell, Lange (1995), “Computer programs for multilocus haplotyping of general pedigrees”, American Journal of Human Genetics, 56(6):1506-1507
• Sobel, Lange, O’Connell, Weeks (1996), in Genetic Mapping and DNA Sequencing , Vol 81 in The IMA Volumes in Mathematics and its Applications, eds TP Speed, MS Waterman (Springer-Verlag), pages 49-63.
• Sobel, Lange (1996), “Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics”, American Journal of Human Genetics, 58(6):1323-1337
• Sobel, Sengul, Weeks (2001), Human Heredity, 52:121-131.
• Sobel, Papp, Lange (2002), “Detection and integration of genotyping errors in statistical genetics”, American Journal of Human Genetics, 70(2):496-508. [ html]
• SIMWALK manual
• FAQ-O-MATIC: http://watson.hgen.pitt.edu/fom-serve/cache/20.html