-q removes header (only if -f is not also chosen)
-n new sample size
-f prints out frequency counts of derived mutations at every site
--condition conditions on observing a site as polymorphic in the new sample size
--unrounded returns unrounded frequencies
--folded calculates folded SFS
--version prints version and license information

           -I 'filename' : input name of fasta file(s) (accepts * wildcard).

           -V : for verbose output
           -N : turn end gaps into N's
           -M : turn all characters except A,C,G,T,_ into N's
           -O : outputs to file 'filename'.out instead of stdout
           -C : changelog since version 1.0
           -S : splits alignment into separate files for groups of sequence ID's
           -G : replaces Genbank ID's with species name (requires Bioperl installation)

ktohap.pl -i <INFILE> -o <OUTFILE> <OPTIONS>

Where <INFILE> is a file in the default Genome Studio output format
and <OUTFILE> is the base name of the hapmap-formatted output file.

Also requires a file called “snpdata.txt” that has information on SNP locations and types, in the following format:

PZE0000200501   0       4894262 hapmap
PZE0000344524   0       4921654 hapmap
PZE0008211605   0       2572930 hapmap

Where first column is SNP name, then chromosome, then position on chromosome, then SNP type.

Optional flags include:

-f	<FORMAT> Currently only accepts teh default \"hapmap\" but other formats may be available soon
-d Makes ktohap report both alleles instead of treating heterozygotes as ambiguity codes.
--inst <NAME> Defines institution column.  Default is UCD
--panel <NAME> Defines panel column.  Default is \"NA\";

HapToTab version 2.1 can be run as follows:

HapToTab.pl <INFILE> <--snp or --bp> <INT> <OPTIONS>

Where <INFILE> is a file in hapmap format.  
HapToTab needs to know the window size either in SNPs or bp (e.g. --snp 100 or --bp 10000).  
A negative number for SNPs will run HapToTab using only one window for the whole file.  
The following options are available:

--g <NAME> name the group you are running haptotab on.  default is \"all\"
--maxdip format the output files for Hudson's maxdip program
--maxhap format the output files for Hudson's maxhap program
--nohets remove all heterozygotes (code as missing data)
--out file has an outgroup (assumes the last column in the hapmap file)
--freq <INT> filters out all SNPs with a frequency less than INT in the data\n\n";