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Programs Available from Steve DiFazio Genomap.pl Combines genotyper output files and produces MapMaker input. Also identifies probable null alleles, checks for possible genotyping errors, analyzes segregation distortion, and determines parental origin of alleles. Requires the congiguration file genomap.cfg See Genomap README file for more information. genojoin.pl Converts output of genomap file to Joinmap format for 'CP' designs. See Genojoin README file for more information. map_recomb.perl Calculates number of recombinations per linkage group and individual. Takes haplotype file as argument in mapmaker format, more or less, with locus, linkage group, position, and 5 columns of filler data before first haplotype. Input data must be tab-delimited text file. There is no theoretical limit on loci or individuals. Usage: perl map_recomb.perl -a inputfile > out.txt, where -a calculates recombinations for all loci, not just 1 locus per bin, inputfile is input file with all genotype info and five columns of other data after locus,lg, and pos. out.txt is the name of the file to save the outputmap_boot.perl Randomly samples loci from mapmaker input file. Usage: perl map_boot.perl -l=loci mapmaker_input > out.txt where loci is the number of loci to pull out of file (default 200), -r allows processing of markers in coupling and repulsion phase, mapmaker_input is mapmaker input file with all genotype info. out.txt is the name of the file to save the outputmap_boot_frame.perl Randomly samples loci from mapmaker input file, maintaining map order and sampling only one marker per binned position. Usage: perl map_boot_frame.perl -l=loci mapmaker input > out.txt where loci is the number of loci to pull out of file (default 200), mapmaker input is mapmaker input file with all genotype info. out.txt is the name of the file to save the output input data must contain locus lg pos genotypesmap_recomb_boot.perl Calculates number of recombinations per linkage group and individual. Takes haplotype file as argument in mapmaker format, more or less, with locus, linkage group, position, and then genotypes in mapmaker format. Input data must be tab-delimited text file. There is no theoretical limit on loci or individuals. Samples in stratified fashion (without replacement) based on number of markers in linkage group. Requires map_boot_frame.perl Usage: perl map_recomb_boot.pl -l=loci -c=cycles -a inputfile > out.txt where loci is the number of loci to sample from file (default 200), cycles is the number of times dataset is to be sampled (default 100) -a results in bootstraps including all loci, not just 1 locus per bin, inputfile is input file with all genotype info and 5 columns of other data after locus,lg, and pos. out.txt is the name of the file to save the outputmapdist.pl Calculates total map length based on poisson expectation for number of linked loci (Hulbert's method) Usage: perl mapdist.pl -l=linkage_cutoff lod_table.txt > out.txt where -linkage_cutoff is the lod score cutoff for linkage, lod_table.txt is the lod table output from mapmaker (with photo mode activated)mapdist_boot.pl Estimates map distance for a given number of loci and LOD cutoff by calling map_boot.perl to subsample loci, and mapmaker to generate linkage tables. Requires map_boot.perl and Mapmaker. Only tested under Solaris 9. May need tweaking of system calls for windows. Usage: mapdist_boot.pl -r -f=configfile -s=lod -l=loci -c=cycles mapmaker_input > out.txt where configfile is an optional configuration file which allows batch processing. format: distance loci cycles -r allows processing of markers in coupling and repulsion phase, loci is the number of loci to pull out of file (default 200), cycles is the number of times dataset is to be sampled (default 100) lod is the cutoff distance for linkage (default 35) mapmaker_input is mapmaker input file with all genotype info. out.txt is the name of the file to save the output Linkage determined from LOD scores only. Finrep A C program primarily by S. Leonardi, with modifications by me. Processes sequence data in Genbank or Fasta format and finds microsatellite repeats. Also includes perl scripts for processing the output from the C program. See Finrep README file for more information. Many other programs and scripts available on request from Steve DiFazio to do such things as |