ddrad

Pipeline to call snps using a reference genome

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

This repository contains a workflow to perform genome-environment association analysis with redundancy analysis.

This repository contains scripts for 3D and 4D demographic models using the program Moments

Random scripts for dealing with ddRAD data, including output from pyRAD

Repository for "Hybridization and inbreeding affect the survival of a critically endangered coral"

Scripts for assembling a linkage map and using QTL mapping to isolate loci underlying failed ovule development in Mimulus nudatus

Code used for a RADseq/GBS (or, more generally, reduced representation sequencing) optimization pilot experiment with several Antarctic animal species.

Plethodontid salamander DNA capture kit

ddRaptor helps you choose optimal ddRAD enzyme pairs by simulating in-silico digests, counting size-filtered fragments, and visualizing results in tables and heatmaps.