{"id":18621301,"url":"https://github.com/4ment/dodonaphy-experiments","last_synced_at":"2025-12-31T14:39:42.340Z","repository":{"id":224662953,"uuid":"762853150","full_name":"4ment/dodonaphy-experiments","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2024-03-30T23:53:29.000Z","size":81,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-05-17T05:09:13.500Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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":"2024-02-24T21:42:38.000Z","updated_at":"2024-03-30T23:53:33.000Z","dependencies_parsed_at":"2024-02-28T06:26:05.954Z","dependency_job_id":"fe288c51-e8e3-49d9-a7e4-cfd616d57db7","html_url":"https://github.com/4ment/dodonaphy-experiments","commit_stats":null,"previous_names":["4ment/dodonophy-experiments","4ment/dodonaphy-experiments"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/4ment/dodonaphy-experiments","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fdodonaphy-experiments","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fdodonaphy-experiments/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fdodonaphy-experiments/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fdodonaphy-experiments/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/dodonaphy-experiments/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fdodonaphy-experiments/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265819926,"owners_count":23833554,"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":[],"created_at":"2024-11-07T04:10:23.863Z","updated_at":"2025-12-31T14:39:42.310Z","avatar_url":"https://github.com/4ment.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dodonaphy-experiments\n\n[![Docker Image CI](https://github.com/4ment/dodonaphy-experiments/actions/workflows/docker-image.yml/badge.svg)](https://github.com/4ment/dodonaphy-experiments/actions/workflows/docker-image.yml)\n\nThis repository contains the pipeline and data sets supporting the results of the following article:\n\nMacaulay M and Fourment M. Differentiable Phylogenetics via Hyperbolic Embeddings with Dodonaphy. [arXiv:2309.11732](https://arxiv.org/abs/2309.11732)\n\n## Dependencies\nYou will need to install [nextflow](https://www.nextflow.io) to run the pipeline. For ease of use the pipeline can be set up with either the package manager [conda](https://conda.io) or [docker](https://www.docker.com). Singularity is another option for running the pipeline on an HPC.\n\n## Download pipeline\n\n    git clone http://github.com/4ment/dodonaphy-experiments.git\n    cd dodonaphy-experiments/\n    chmod +x bin/*.py\n\n## Pipeline without docker/singularity\n\n### Installing dependencies with conda\n    conda env create -f environment.yml\n    conda activate dodonaphy\n    git clone http://github.com/mattapow/hydraPlus.git\n    pip install hydraPlus/\n    git clone http://github.com/mattapow/dodonaphy.git\n    pip install dodonaphy/\n\n### Running the pipeline\n\n    nextflow run main.nf\n\n## Pipeline with docker or singularity\nThere is no need to install dependencies with docker or singularity.\n\n### Running the pipeline with docker\n\n    nextflow run main.nf -profile docker\n\n### Running the pipeline with singularity and PBS\n\n    nextflow -C configs/uts.config run main.nf -profile singularity\n\nSince the pipeline will take weeks to run to completion one should use a high performance computer. An example of a configuration file for pbspro can be found in the [configs](configs/) folder.\n\n## Generating figures\n\nTable 1: Comparison of marginal log-likelihood estimates.\n\n    find results/vi -name samples.t|grep b1|xargs python bin/marginal.py\n\nFigure 2: Difference in maximum log likelihood estimates compared to RAxML across all datasets DS1-8.\n\n    find results/hmap -name \"*.csv\"| xargs python bin/ml_performance.py\n\n\nFigure 3: Variational approximation in $H^3$ compared to MCMC.\n\n    python bin/split_lengths_prepare.py --output branch_lengths_by_treelist_sorted.csv results/vi/DS1/vi/up_nj/d3_lr2_i3_b3/samples.t results/mrbayes/DS1/DS1.nex.run*.t\n    python bin/split_lengths_plot.py branch_lengths_by_treelist_sorted.csv\n\nFigure 4: Effect of the number of boosts on the final SIWAE estimate for DS1.\n\n    find results/vi/DS1 -name vi.log| xargs python bin/SIWAE_boosts.py","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fdodonaphy-experiments","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Fdodonaphy-experiments","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fdodonaphy-experiments/lists"}