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 output
map_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 output
map_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 genotypes
map_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 output
mapdist.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.