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admixturepipeline

A pipeline that accepts a VCF file to run through Admixture

adratio

Classifying sex-linked and autosomal scaffolds using allele-depth ratios computed from pileup data

alb_conch_data

Data and scripts from Douglas et al. Mar. Ecol.

alleles2taghap.pl

Perl script to convert from the .alleles format created by pyRAD to a 'tag haplotype' matrix for input to fineRADstructure

anomaly_zone

Detecting the anomaly zone in trees - modified from Linkem et al 2016

autostreamtree

Stream trees for SNP datasets

ba3-snps-autotune

Python code for automatically tuning mixing parameters in BayesAss3

ba3_output_parser

bayesass3-snps

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

birds

ccm-arm

Digitizing CMM Arm for importing features and point cloud data. Original concept and source code by DZL.

clineplotr

Plot Genomic Clines from BGC and INTROGRESS and Correlate with Environental Variables

cloudbutton-redis-installation

coalhmm

CoalHMM - porting to python 3

conda-recipes

consgen2018

Repository for the Spring 2018 course in Conservation Genetics (BIOL-5174) at the University of Arkansas

douglas_lab_adapters

Repository for designing our RAD and UCE adapters.

ecopy

Python tools for ecological data analyses

excelparsers

Random parsers for automating terrible lab-specific tasks for the Douglas Lab at University of Arkansas. Mostly saved here so I can reference them later. They are NOT written to be user-friendly, nor is any documentation provided.

fgtpartitioner

Parsimonious delimitation of large SNP datasets using the four gamete test

file_converters

File conversion scripts for DNA sequence data

floppybirb

A Java implementation of "Flappy Bird" which I have modified according to my own tastes. This was my first Java project (ever)- so if you decide to take a look at this code and have any pointers, feel free to send them my way

floppybirbai

A version of my Java "Floppy Birb" game which implements a recursive AI to play the game for you

fragmatic

Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods

freyja

Depth-weighted De-Mixing

genetic-variant-detection-in-cell-pops

Snakemake workflow for detecting genetics variants (snp, indels, and structural variants) in cell populations

ggoutlier

gila_simulations

My top secret repository for my SLiM scripts >:)

haplotools

Python scripts to create input files for haplotype reconstruction in Phase, parse outputs, and perform some other manipulations with haplotypes/ diplotypes