{"id":15465688,"url":"https://github.com/thibaultlatrille/micmac","last_synced_at":"2026-01-08T00:05:56.029Z","repository":{"id":198045892,"uuid":"410913601","full_name":"ThibaultLatrille/MicMac","owner":"ThibaultLatrille","description":" Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes ","archived":false,"fork":false,"pushed_at":"2024-09-26T07:38:02.000Z","size":19745,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-09T00:05:22.248Z","etag":null,"topics":["scientific-papers","snakemake-workflow"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1093/jeb/voae084","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ThibaultLatrille.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2021-09-27T14:16:30.000Z","updated_at":"2024-09-26T07:38:09.000Z","dependencies_parsed_at":"2023-12-06T17:27:32.914Z","dependency_job_id":"2dc503e7-78a9-45ee-8684-71795da9c5e0","html_url":"https://github.com/ThibaultLatrille/MicMac","commit_stats":{"total_commits":85,"total_committers":3,"mean_commits":"28.333333333333332","dds":0.2941176470588235,"last_synced_commit":"967bf9030b3b011c166db89a73119901d7eda805"},"previous_names":["thibaultlatrille/micmac"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FMicMac","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FMicMac/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FMicMac/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FMicMac/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ThibaultLatrille","download_url":"https://codeload.github.com/ThibaultLatrille/MicMac/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":235134867,"owners_count":18941328,"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":["scientific-papers","snakemake-workflow"],"created_at":"2024-10-02T01:02:37.225Z","updated_at":"2025-10-03T13:31:01.481Z","avatar_url":"https://github.com/ThibaultLatrille.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"**Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes**,\\\nThibault Latrille, Melodie Bastian, Theo Gaboriau, Nicolas Salamin,\\\n_Journal of Evolutionary Biology_, voae084,\\\n2024,\\\n[doi.org/10.1093/jeb/voae084](https://doi.org/10.1093/jeb/voae084)\n\n**Compiled binaries and instructions for BayesCode are available at [github.com/ThibaultLatrille/bayescode](https://github.com/ThibaultLatrille/bayescode)**\n\n# MicMac\n\nThis repository is meant to provide the necessary scripts and data to reproduce the figures shown in the manuscript.\\\nThe experiments can either run on a local computer or in a cluster configuration (slurm).\\\nThe experiments are meant to run on Linux/Unix/MacOS operating systems.\n\n## Repository structure\n\nThe repository is split into six main directories, some of which have subdirectories.\\\nWithin each directory is a `README.md` file which summarizes the purpose of that directory.\\\nThe main directories are as follows:\n\n### **`data_empirical`**\nThis folder contains the snakemake pipeline (`Snakefile`) and data to run the empirical analysis shown in table 1.\\\nThe details are described in the `README.md` file in the `data_empirical` folder.\n\n### **`data_simulated`**\nThis folder contains the snakemake pipeline (`Snakefile`) and data to run simulated analysis shown in figure 3 and S2.\\\nThe details are described in the `README.md` file in the `data_simulated` folder.\n\n### **`manuscripts`**\nThis folder contains the different versions of the manuscript (.tex), supplementary material (.tex) and figures (.pdf).\n\n### **`scripts`**\nThis folder contains the python scripts used by the snakemake pipelines to run the analysis (see `data_empirical` and `data_simulated`).\n\n### **`simulator`**\nThis folder contains the simulation program to generate the data for the simulated analysis, required to run the experiments in the `data_simulated` folder.\\\nThe details to compile the simulation program and its usage are described in the `README.md` file in the `simulator` folder.\n\n### **`utils`**\nThis folder contains the [BayesCode](https://github.com/ThibaultLatrille/bayescode) software, necessary to run the analysis in the `data_simulated` and `data_empirical` folders.\\\nThe details to install BayesCode and its usage are described in the `README.md` file in the `utils` folder.\n\n## Installation and dependencies\n\n### Python and snakemake dependencies\n\nInstall python3, snakemake and the necessary python packages.\n\n```\nsudo apt install -qq -y python3-dev python3-pip\npip3 install snakemake scipy numpy matplotlib pandas ete3 bio statsmodels --user\n```\n\n### BayesCode and simulator dependencies\nThe [BayesCode](https://github.com/ThibaultLatrille/bayescode) software is necessary to run the analysis in the `data_simulated` and `data_empirical` folders.\\\nSee the `README.md` file in the `utils` folder to install BayesCode.\n\nThe simulator program is necessary to run the experiments in the `data_simulated` folder.\\\nSee the `README.md` file in the `simulator` folder to compile the simulation program.\n\n## Licence\n\nThe MIT License (MIT)\n\nCopyright (c) 2023 Thibault Latrille\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated\ndocumentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the\nrights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit\npersons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the\nSoftware.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE\nWARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR\nCOPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR\nOTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthibaultlatrille%2Fmicmac","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthibaultlatrille%2Fmicmac","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthibaultlatrille%2Fmicmac/lists"}