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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

Science Score: 23.0%

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    Links to: arxiv.org
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    Low similarity (6.5%) to scientific vocabulary

Keywords

data data-visualization marginal-likelihood phylogenetics
Last synced: 9 months ago · JSON representation

Repository

19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology

Basic Info
  • Host: GitHub
  • Owner: 4ment
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 117 KB
Statistics
  • Stars: 4
  • Watchers: 4
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Topics
data data-visualization marginal-likelihood phylogenetics
Created about 8 years ago · Last pushed about 7 years ago
Metadata Files
Readme

README.md

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.

Requirements

physher

To reproduce the analysis the release 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.

Owner

  • Name: Mathieu Fourment
  • Login: 4ment
  • Kind: user
  • Location: Australia
  • Company: University of Technology Sydney

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Dependencies

Dockerfile docker
  • debian stretch build