{"id":18621312,"url":"https://github.com/4ment/marginal-experiments","last_synced_at":"2025-04-11T02:31:41.644Z","repository":{"id":66955325,"uuid":"131789442","full_name":"4ment/marginal-experiments","owner":"4ment","description":"19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology","archived":false,"fork":false,"pushed_at":"2019-04-25T01:53:09.000Z","size":120,"stargazers_count":4,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-25T08:22:58.067Z","etag":null,"topics":["data","data-visualization","marginal-likelihood","phylogenetics"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/4ment.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-05-02T02:48:13.000Z","updated_at":"2020-10-26T06:05:40.000Z","dependencies_parsed_at":"2023-02-21T05:45:42.728Z","dependency_job_id":null,"html_url":"https://github.com/4ment/marginal-experiments","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fmarginal-experiments","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fmarginal-experiments/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fmarginal-experiments/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fmarginal-experiments/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/marginal-experiments/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248329606,"owners_count":21085566,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["data","data-visualization","marginal-likelihood","phylogenetics"],"created_at":"2024-11-07T04:10:30.079Z","updated_at":"2025-04-11T02:31:41.637Z","avatar_url":"https://github.com/4ment.png","language":"Python","readme":"# 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology\n\nThis repository contains the pipeline and data sets supporting the results of the following article:\n\nFourment 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).\n\n# Requirements\n\n## [physher](https://github.com/4ment/physher)\n\nTo 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.\n\n# Running the simulations\n\n``` shell\ncd marginal-experiments\npython run_simulations.py\n```\n\nor using Docker (no need to install physher)\n\n```shell\ncd marginal-experiments\ndocker pull 4ment/marginal-experiments\ndocker run -v $PWD:/data 4ment/marginal-experiments\n```\n\nThe simulations will take several weeks to complete. Multiple directories will be produced (DS1, DS2, DS3, DS4, DS5).\n\n\n# Parsing results\n\n```shell\nRscript -e 'rmarkdown::render(\"DS.Rmd\")'\n``` \n\nThe script will generate the file `DS.pdf`.","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fmarginal-experiments","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Fmarginal-experiments","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fmarginal-experiments/lists"}