Data and code associated with: What Came First? Wright AM, Lyons KM, Hillis DM, Brandley MB.

Exploratory notebooks: IPython notebooks used for exploratory analysis. These scripts are not used in the main pipeline, but used to explore data. Values from these exploratory notebooks are reported in the paper, but not used explicitly a pipeline step. Also included are interactive vesions of pipeline pieces.
Main pipeline: This is the main pipeline used to create the main results in the paper. Makefile reproduces full analysis. To do this, clone the repository, change directories into it and type make
Dependencies:
- R:
  - Diversitree
- Python:
  - Pandas
  - Matplotlib
  - Dendropy
Note: Running the full pipeline with make is a multiple-hour process. Picking the steps of interest out of the Scripts directory is almost certainly more useful.

Installing Dependencies

Install gsl (pre-requisite)

$ sudo apt-get install gsl-bin libgsl0-dev

Now install diversitree

install.packages(c('diversitree'))

Name		Name	Last commit message	Last commit date
Latest commit History 73 Commits
.ipynb_checkpoints		.ipynb_checkpoints
Data		Data
ExploratoryNotebooks		ExploratoryNotebooks
Figures		Figures
Scripts		Scripts
annotated		annotated
newtrees		newtrees
unwanted figs		unwanted figs
.Rhistory		.Rhistory
.gitignore		.gitignore
Dockerfile		Dockerfile
LICENSE		LICENSE
Makefile		Makefile
RAxML_bestTree.result		RAxML_bestTree.result
README.md		README.md
Which Came First.docx		Which Came First.docx
bisse.r		bisse.r
input_fasta		input_fasta
model_params.csv		model_params.csv
model_params_sept.csv		model_params_sept.csv
ovip_support.csv		ovip_support.csv
plot_dist.py		plot_dist.py
plot_support.py		plot_support.py
prunetree.py		prunetree.py
pv_tip		pv_tip
pyron_Scaledtree.tre		pyron_Scaledtree.tre
rfdist.py		rfdist.py
vivip_support.csv		vivip_support.csv