Perl
HapToTab
HapToTab converts hapmap data files into polytables suitable for analysis in libsequence, Sofos, etc. Read More...
ktohap
ktohap converts the default Illumina Genome Studio output format to a hapmap data format.
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pattern_finder
pattern_finder identifies patterns a,b,c and d of triplet and quadruplet sites (Padhukasahasram 2004) from simulated data in ms format. Read More...
SoFoS
SOFOS allows calculation and rescaling of the site frequency spectrum from polymorphism data. Read More...
COWDUDE
COWDUDE (catalogue operation with database user data entry) is a perl script that interfaces with a mysql database to manage germplasm inventory tracking and barcode creation. Read More...
fastU
fastU performs a number of minor fasta-handling utilities Read More...
Theta Curve
ThetaCurve is a perl script for calculating the a multilocus maximum likelihood value of the per locus Watterson's estimator of the population mutation rate theta. Read More...
RminCutter
RminCutter is a perl script to estimate Hudson & Kaplan's rmin from a standard fasta file, then cut the file into semi-independent regions of sequence with no internal recombination (if you believe that sort of thing). Allows choice of 3 definitions of intervals for output. Read More...
Ewens Sampler
A simple perl script to generate the expected site frequency spectrum for a sample of size n for a population mutation rate of θ. I am no longer entirely sure why you would want to do this. Read More...