LDit

Filed in: R
Simple R code to plot LD decay. Read More...

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SFS

Filed in: Perl
SFS is a simple perl scrip to calculate the Site Frequency Spectrum from a polytable (a table showing polymorphic SNPs).
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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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eight_zygote

Filed in: R
An analog of the 4-gamete test for dominant genotypic data.
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HBK_permute

Filed in: C++
A modification of the HBKpermute program from K. Thornton’s analysis package.
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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...

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SITESpipe

Filed in: Perl

Perl scripts to convert and run Jody Hey's SITES program. Read More...

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msnsam

Filed in: C++
A modification of Dick Hudson's ms program. Read More...

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fastU

Filed in: Perl
fastU performs a number of minor fasta-handling utilities Read More...

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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...

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Geneious Converter

Filed in: Perl
A simple perl script that converts files in the .genious format to fasta format.

Runs with the following command:

genious_to_fasta.pl -i

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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...

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Metapopulation Graphs

Filed in: R
R Code to graph the figures from van Heerwaarden, van Eeuwijk, and Ross-Ibarra 2009.
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SimDataTBS

Filed in: C++
Allow reading in the tbs line from ms-output. Read More...

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SimDataDip

Filed in: C++
Files to allow conversion of ms-style output to dominant diploid data. Read More...

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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...

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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...

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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...

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