laduplessis / beast2_bdskysa_ebov_example

Example for BEAST v2.5 paper

BEAST v2.5 West Africa Ebola example

Please contact Louis du Plessis ([e-mail]) for any questions.

Summary

Phylodynamics example for BEAST 2.5 paper using data from the West African Ebola dataset. The example uses a sampled-ancestor birth-death skyline to infer population dynamics. This can also double as a bModelTest example.

Full documentation is inside the doc/ directory.

Reproducing results

Follow the workflows in workflows/

1. data_partition.md: Extract and process coding and noncoding regions of the full alignment.
2. extract_datasdets.rmd: Extract particular datasets from alignment.
3. extract_sampling.rmd: Extract empirical sampling proportions from datasets.
4. beast_runs.md: Create, run and combine BEAST XMLs.
5. plot_figures.md: Plot output figures.

License

The content of this project itself is licensed under the Creative Commons Attribution 3.0 Unported license, and the underlying source code used to format and display that content is licensed under the GNU General Public License v3.