Deren and Sarah learning about Canarium
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Figures
manuscript
CanEnd_traits.csv
README.md
Table_S1.csv
Table_S2.csv
Table_S3.csv
Table_S4.csv
Table_S5.csv
Table_S6.csv
Table_S7.csv
nb-1-ipyrad-assembly.ipynb
nb-2-phylogeny-inference.ipynb
nb-3-concordance.ipynb
nb-4-BPP.ipynb
nb-5-structure.ipynb
nb-6-abba-baba.ipynb
nb-7-BPP-unit-conversion.ipynb

README.md

Canarium species tree inference and delimitation

DOI

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.

:🚀:

  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