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analysis_dadi
analysis_dtests
analysis_pyrad/stats
analysis_raxml
analysis_structure
figures
RAD_geos.txt
README.md added doi for code repo Jul 6, 2015
SraRunTable.txt
models_simple.png
nb1_virentes_assembly.ipynb
nb2_virentes_trees.ipynb
nb3_virentes_dtests.ipynb
nb4_virentes_populations.ipynb
nb5_virentes_dadi.ipynb

README.md

Reproducible science for live oak introgression study

This code repository is archived: DOI

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

Assembled data sets

DOI
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

This notebook contains code used for D-statistic analyses performed in pyRAD.
3. D-statistics introgression analysis notebook

This notebook contains code used for Structure and TreeMix analyses.
4. Population analyses notebook

This notebook contains code used for fitting demographic models in dadi_.
5. dadi introgression analysis notebook