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.
This notebook contains code to download sequence data and assemble it in pyRAD v. 2.13.
The assembled data sets are hosted on Zenodo at the DOI above. These data sets are used for analyses contained in the notebooks below.
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