## Reproducible science for live oak introgression study

### This code repository is archived: [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.19476.svg)](http://dx.doi.org/10.5281/zenodo.19476)

### Directions

This repository contains several IPython notebooks with code to reproduce 
all analyses in the manuscript "Historical introgression among the American live oaks and the comparative nature of tests for Introgression" (Eaton et al. 2015). The notebooks can be viewed by opening the links below.  

### Notebooks  

#### Data assembly 
This notebook contains code to download sequence data and assemble it in pyRAD v. 2.13.  
1. [RAD assembly notebook](http://nbviewer.ipython.org/github/dereneaton/virentes/blob/master/nb1_virentes_assembly.ipynb)  

#### Assembled data sets  
[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.19475.svg)](http://dx.doi.org/10.5281/zenodo.19475)  
The assembled data sets are hosted on `Zenodo` at the DOI above. These data sets are used for analyses contained in the notebooks below. 

#### Analyses  
This notebook contains code used for _RAxML_ analyses.  
2. [Phylogenetic analysis notebook](http://nbviewer.ipython.org/github/dereneaton/virentes/blob/master/nb2_virentes_trees.ipynb)  

This notebook contains code used for D-statistic analyses performed in _pyRAD_.  
3. [D-statistics introgression analysis notebook](http://nbviewer.ipython.org/github/dereneaton/virentes/blob/master/nb3_virentes_dtests.ipynb)  

This notebook contains code used for _Structure_ and _TreeMix_ analyses.  
4. [Population analyses notebook](http://nbviewer.ipython.org/github/dereneaton/virentes/blob/master/nb4_virentes_populations.ipynb)  

This notebook contains code used for fitting demographic models in _dadi__.  
5. [_dadi_ introgression analysis notebook](http://nbviewer.ipython.org/urls/raw.github.com/dereneaton/virentes/master/nb5_virentes_dadi.ipynb)