{"id":15465682,"url":"https://github.com/thibaultlatrille/redqueen","last_synced_at":"2026-03-19T07:34:32.072Z","repository":{"id":85542132,"uuid":"50335290","full_name":"ThibaultLatrille/RedQueen","owner":"ThibaultLatrille","description":"The Red-Queen model of recombination hot-spot evolution: a theoretical investigation.","archived":false,"fork":false,"pushed_at":"2022-03-22T13:42:17.000Z","size":109838,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-22T17:39:47.719Z","etag":null,"topics":["mathematical-modelling","scientific-publications","simulation"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1098/rstb.2016.0463","language":"TeX","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/ThibaultLatrille.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":"2016-01-25T07:57:47.000Z","updated_at":"2022-05-13T21:11:27.000Z","dependencies_parsed_at":null,"dependency_job_id":"cc4fb9ac-155c-4c6c-bebd-7d9d9a9fbe5b","html_url":"https://github.com/ThibaultLatrille/RedQueen","commit_stats":{"total_commits":174,"total_committers":5,"mean_commits":34.8,"dds":0.5459770114942528,"last_synced_commit":"172a03c327a95dce567842e17fcb4a99aa99d1c4"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FRedQueen","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FRedQueen/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FRedQueen/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ThibaultLatrille%2FRedQueen/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ThibaultLatrille","download_url":"https://codeload.github.com/ThibaultLatrille/RedQueen/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240014012,"owners_count":19734178,"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":["mathematical-modelling","scientific-publications","simulation"],"created_at":"2024-10-02T01:02:31.904Z","updated_at":"2025-10-08T13:18:16.872Z","avatar_url":"https://github.com/ThibaultLatrille.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"**The Red-Queen model of recombination hot-spot evolution: a theoretical investigation,**\\\n_Thibault Latrille, Laurent Duret, Nicolas Lartillot_,\\\nPhil. Trans. R. Soc. B,\\\nhttp://doi.org/10.1098/rstb.2016.0463\n\n#### Code to reproduce the figures showed in the manuscript\nRequirements:\n - Python 3.5\n - numpy\n - scipy\n - matplotlib\n\n```\n$ python3 redQueen.py -n 100000\n```\n\noptional arguments:\n  - -c \u003cnbr of cpu\u003e, --cpu \u003cnbr of cpu\u003e\n  \n                        Number of CPU available for parallel computing\n                        (default: 4)\n  - -t \u003ctime of simulation\u003e, --time \u003ctime of simulation\u003e\n  \n                        The number of steps of simulations (proportional to\n                        time) (default: 50)\n  - -w \u003cThe wall time\u003e, --wall_time \u003cThe wall time\u003e\n  \n                        The wall time (in seconds) of the whole computation\n                        (default: inf)\n  - -r \u003crange order of magnitude\u003e, --range \u003crange order of magnitude\u003e\n  \n                        The order of magnitude to span around the focal\n                        parameters (default: 2)\n  - -s \u003cnumber of simulations\u003e, --simulations \u003cnumber of simulations\u003e\n  \n                        number of independent simulations to span (default:\n                        32)\n  - -n \u003cpopulation size\u003e, --population_size \u003cpopulation size\u003e\n  \n                        Effective population size (default: 100000)\n  - -u \u003cPrdm9 mutation rate\u003e, --mutation_rate_prdm9 \u003cPrdm9 mutation rate\u003e\n  \n                        The mutation rate of Prdm9 (multiplied by 10e-6)\n                        (default: 1.0)\n  - -v \u003cHotspots mutation rate\u003e, --mutation_rate_hotspot \u003cHotspots mutation rate\u003e\n  \n                        The mutation rate of hotspots (multiplied by 10e-7)\n                        (default: 10.0)\n  - -f \u003cfitness\u003e, --fitness \u003cfitness\u003e\n  \n                        The fitness either 'linear', 'sigmoid', 'power' or\n                        'poisson' (default: power)\n  - -a \u003calpha\u003e, --alpha \u003calpha\u003e\n  \n                        The parameter alpha of the fitness (default: 0.1)\n                        \n                        - is not used if the fitness is 'linear'.\n                        - is the power exponent if the fitness is 'power'.\n                        - is the exponential parameter if the fitness is 'poisson'.\n                        - is the inflexion point if the fitness is 'sigmoid'. \n  - -d \u003credraw figures\u003e, --redraw \u003credraw figures\u003e\n  \n                        Draw the figures using the file 'Batch.p' (default:\n                        False)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthibaultlatrille%2Fredqueen","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthibaultlatrille%2Fredqueen","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthibaultlatrille%2Fredqueen/lists"}