https://github.com/4ment/marginal-experiments
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
https://github.com/4ment/marginal-experiments
data data-visualization marginal-likelihood phylogenetics
Last synced: 10 months ago
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19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
- Host: GitHub
- URL: https://github.com/4ment/marginal-experiments
- Owner: 4ment
- Created: 2018-05-02T02:48:13.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-04-25T01:53:09.000Z (almost 7 years ago)
- Last Synced: 2025-03-25T08:22:58.067Z (10 months ago)
- Topics: data, data-visualization, marginal-likelihood, phylogenetics
- Language: Python
- Homepage:
- Size: 117 KB
- Stars: 4
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
This repository contains the pipeline and data sets supporting the results of the following article:
Fourment M, Magee A, Whidden C, Bilge A, Matsen IV FA, Minin VN. 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology. [arXiv:1811.11804](https://arxiv.org/abs/1811.11804).
# Requirements
## [physher](https://github.com/4ment/physher)
To reproduce the analysis the release [marginal-v1.1](https://github.com/4ment/physher/releases/tag/marginal-v1.1) should be used and the executable should be located in the `bin` directory.
# Running the simulations
``` shell
cd marginal-experiments
python run_simulations.py
```
or using Docker (no need to install physher)
```shell
cd marginal-experiments
docker pull 4ment/marginal-experiments
docker run -v $PWD:/data 4ment/marginal-experiments
```
The simulations will take several weeks to complete. Multiple directories will be produced (DS1, DS2, DS3, DS4, DS5).
# Parsing results
```shell
Rscript -e 'rmarkdown::render("DS.Rmd")'
```
The script will generate the file `DS.pdf`.