HapToTab
Filed in: Perl
HapToTab converts hapmap data files into polytables suitable for analysis in libsequence, Sofos, etc. Read More...
ktohap
Filed in: Perl
ktohap converts the default Illumina Genome Studio output format to a hapmap data format.
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pattern_finder
Filed in: Perl
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
Filed in: Perl
SOFOS allows calculation and rescaling of the site frequency spectrum from polymorphism data. Read More...
COWDUDE
Filed in: Perl
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...
WFT?
Filed in: R
WFT? (For Wright-Fisher Tracker?) is a simple R function that does binomial sampling to show genetic drift.
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HBK_permute
Filed in: C++
msstats_fst
Filed in: C++
A modification of K. Thornton’s msstats program that calculates Weir & Cockerham’s Fst estimator from ms simulations.
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IAMSAM
Filed in: C++
IAMSAM is a forward simulation to test predictions of the Indel Associated Mutation model. Read More...
Theta Curve
Filed in: Perl
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...
DiceDist
Filed in: C++
This program calculates Dice's distance measure among all pairs of individuals from a population, and outputs a triangle distance matrix suitable for use in Neighbor or other phylogeny programs. Read More...
Metapopulation Graphs
Filed in: R
SimDataDip
Filed in: C++
Files to allow conversion of ms-style output to dominant diploid data. Read More...
TwoDen
Filed in: R
A function to plot the joint density of two vectors on a grid. Basically it plots 2-D histograms.
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TwoBar
Filed in: R
A quick and dirty little function to plot two vectors on the same barplot.
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ABCX
Filed in: Bash
ABCX is a simple bash script to exemplify the Approximate Bayesian Computation approach to population genetic analysis. Read More...
RminCutter
Filed in: Perl
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
Filed in: Perl
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...