Canarium species tree inference and delimitation

Jupyter notebooks with documented code to reproduce results from "Reconciling Species Diversity in a Tropical Plant Clade (Canarium; Burseraceae)" by Federman et al. (2018).

Notebook 1 includes code to download the raw archived genomic data and assemble it with ipyrad, and subsequent notebooks include code to reproduce downstream analyses. All code makes use of ipyrad and the ipyrad analysis toolkit, and the notebooks include instructions for installing required software using conda.

::rocket::

1. ipyrad assembly notebook
2. phylogenetic analysis notebook
3. concordance analysis notebook
4. bpp spp. delimitation notebook
5. structure analysis notebook
6. abba-baba notebook
7. bpp calibration notebook