A perl script to estimate Hudson & Kaplan's rmin from a standard fasta file, then cut the file into regions with no 4-gamete violation. Note that a lack of 4-gamete violation does NOT mean there was no recombination! An example fasta file seqfile.txt is included.
Allows choice of 3 definitions of intervals for output.
Run the program with "perl rmincutter.pl -i filename" (accepts wildcard).
Input file must be fasta-formated with all the sequence on one line. Output is printed to filename_1.out, filename_2.out, etc.
-v : for verbose output
-q : suppress top header line on output files
-s : suppress warning to STDERR
-f : add '.fasta' to the end of output files for easier manipulation by other programs
-m : for smaller set of recombination intervals
This option forces reduction of recombination intervals to the smallest range of
sequence which can explain the observed data. It does NOT give regions in
which recombination DID occur.
-g : skip sites with gaps
-p : uses a 'greedy' algorithm which uses all SNPs
As a result, each region is likely to still encompass a recombination
event and thus violate the assumptions of many models.
-n : skip sites with missing data
-t : skip sites with >2 bases segregating data
-c : changelog since version 1.0
Hudson, R. and N. Kaplan. 1985. Genetics 111:147-164