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Welcome to the rtd wiki!

The scripts in this repository are intended for analysis of RADseq data in the absence of a reference genome sequence (see Peterson et al 2012 for details of the algorithms implemented here)

Throughout this wiki and in the design of the scripts themselves, a working understanding of the linux/unix environment is assumed. There are many good basic references for getting started with linux and unix, we found this book helpful: Unix and Linux: Visual QuickStart Guide (4th Edition) by Deborah S. Ray and Eric J. Ray

This wiki is divided into four sections:

Getting Started: Accessory Programs

Getting Started: Configure RTD

Running RTD Pipeline

Simulations and Evaluation