Fastslink on Helix
Description
The FastSLINK program is the merger of code from FASTLINK version 2.x to the slink program, by Alejandro Schaffer and Dan Weeks. 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.
Version
Type slink on command line
Sample session
% slink Program SLINK version 2.51 The program constants are set to the following maxima: 8 loci in mapping problem (maxlocus) 11 alleles at a single locus (maxall) 157 recombination probabilities (maxneed) 50000 maximum of censoring array (maxcensor) 180 haplotypes = n1 x n2 x ... where ni = current # alleles at locus i 16290 joint genotypes for a female 16290 joint genotypes for a male 2000 individuals in all pedigrees combined (maxind) 150 pedigrees (maxped) 11 binary codes at a single locus (maxfact) 3 quantitative factor(s) at a single locus 10 liability classes 11 binary codes at a single locus 1.00 base scaling factor for likelihood (scale) 2.00 scale multiplier for each locus (scalemult) 0.00000 frequency for elimination of heterozygotes (minfreq) ******************************************************* This is SLINK, which is a general simulation program. The output file pedfile.dat may be analyzed with the companion programs MSIM, LSIM, and ISIM. ******************************************************* Reading SIMDATA.DAT YOU ARE USING LINKAGE/SLINK (V2.51) WITH 2-POINT AUTOSOMAL DATA Reading SIMPED.DAT Reading SLINKIN.DAT The random number seed is: 29876 The number of replications is: 200 The requested proportion of unlinked families is: 0.000 The trait locus is locus number: 1 Summary Statistics about simped.dat Number of pedigrees 1 Number of people 4 Number of females 2 Number of males 2 There were 0 in category: Marker Unknown; Trait original There were 0 in category: Marker Available; Trait simulated There were 4 in category: Marker Available; Trait original There were 0 in category: Marker Unknown; Trait simulated ----------------------------------- LINKED ORDER OF LOCI: 1 2 ----------------------------------- ----------------------------------- TRUE THETAS FOR LINKED ORDER 0.010000 ----------------------------------- ----------------------------------- UNLINKED ORDER OF LOCI: 1 2 ----------------------------------- ----------------------------------- TRUE THETAS FOR UNLINKED ORDER 0.500000 ----------------------------------- Beginning simulations... . Maxneed may be reduced to 7 Maxcensor can be reduced to -32767 Elapsed Time for one replicate = 0.00 seconds Estimated Time to finish = 0.00 minutes = 0.00 hours ........*.........*.........*.........*.........* 50 replicates generated .........*.........*.........*.........*.........* 100 replicates generated .........*.........*.........*.........*.........* 150 replicates generated .........*.........*.........*.........*.........* 200 replicates generated Elapsed Time = 0.00 min. or 0.00 hours ----------------------------------- Actual proportion of unlinked families: 0.000 SLINK has completed 200 replicates.
Documentation
http://watson.hgen.pitt.edu/docs/SLink.html