{"id":47738038,"url":"https://github.com/kamilsjaron/conjunction","last_synced_at":"2026-04-02T23:04:17.144Z","repository":{"id":23041516,"uuid":"26394497","full_name":"KamilSJaron/Conjunction","owner":"KamilSJaron","description":"Simulator of secondary CONtact using Fisher's JUNCTION representation of genome admixture.","archived":false,"fork":false,"pushed_at":"2018-05-31T21:04:57.000Z","size":479,"stargazers_count":1,"open_issues_count":7,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-12-06T21:50:46.142Z","etag":null,"topics":["admixture","biology","genome-admixture","hybrid-zone","population-genetics","secondary-contact","simulator"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KamilSJaron.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}},"created_at":"2014-11-09T12:09:13.000Z","updated_at":"2018-05-31T21:04:59.000Z","dependencies_parsed_at":"2022-08-05T20:15:50.091Z","dependency_job_id":null,"html_url":"https://github.com/KamilSJaron/Conjunction","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/KamilSJaron/Conjunction","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KamilSJaron%2FConjunction","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KamilSJaron%2FConjunction/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KamilSJaron%2FConjunction/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KamilSJaron%2FConjunction/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KamilSJaron","download_url":"https://codeload.github.com/KamilSJaron/Conjunction/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KamilSJaron%2FConjunction/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31318160,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-02T21:35:00.834Z","status":"ssl_error","status_checked_at":"2026-04-02T21:34:59.806Z","response_time":89,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["admixture","biology","genome-admixture","hybrid-zone","population-genetics","secondary-contact","simulator"],"created_at":"2026-04-02T23:04:16.171Z","updated_at":"2026-04-02T23:04:17.091Z","avatar_url":"https://github.com/KamilSJaron.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n![logo](logo/Conjunction.png)\n\nthe simulator of secondaty CONtact using Fisher's JUNCTION model of genome admixture. It is a direct descendant of forsim, simulator writen for my [Master thesis](http://is.muni.cz/th/376090/prif_m/thesis_jaron_zadani.pdf).\n\n## Build\n\nThe software was developed and tested on OS X and Linux and it has not been tested for windows.\n\n#### Quick\n\nOpen a terminal, download repository\n\n```\ngit clone https://github.com/KamilSJaron/Conjunction\n```\n\nenter the folder and build Conjunction by\n\n```\ncd Conjunction \u0026\u0026 make\n```\n\nThe fully operational executable `conjunction` should be created and prepared for use. You can install `conjunction` to by\n\n```\nmake install\n```\n\nwhich will copy the binary to `/usr/local/bin`. If you wist to install `conjunction` to an alternative place you can type\n\n```\nmake install INSTAL_PREFIX=/home/slim/\n```\n\nand it will be installed in provided path/bin. In my example `/home/slim/bin`.\n\n#### Testing\n\nTravis build \u0026 unit test of `master` branch : [![master_build](https://travis-ci.org/KamilSJaron/Conjunction.svg?branch=master)](https://travis-ci.org/KamilSJaron/Conjunction/branches)\nTravis build \u0026 unit test of `dev` branch : [![dev_test](https://travis-ci.org/KamilSJaron/Conjunction.svg?branch=dev)](https://travis-ci.org/KamilSJaron/Conjunction/branches)\n\nSeveral unit tests are implemented in separated binary. To execute the unit test on your computer\n\n```\nmake test\n```\n\nwill compile testing binary, execute tests and delete testing binary if tests passed.\n\n## Usage\n\nThe software reads a setting file (`setting.txt` by default), the specification of the simulation is read from there. The template is delivered with the software, therefore simple `conjunction` should perform a set of sumulations. For details of check [setting file](setting.txt) or wikipage [setting](https://github.com/KamilSJaron/Conjunction/wiki/setting).\n\n```{bash}\nconjunction [--version] [--help] [setting.txt] 1\u003e summary.out 2\u003e simulation_log.err\n```\n\nThe log of the simulation is streamed to standard error stream. The basic output of simulation is streamed to standard output stream. If other type of output is desired it has to be set in setting, details can be found at corresponding wikipage describing [output](https://github.com/KamilSJaron/Conjunction/wiki/output).\n\n## Mechanisms of simulations\n\nThe simulator is restricted to secondary contact hybrid zones where reduced fitness of hybrids is caused purely by genetic background. The representation of individuals currently does not allow new mutations in simulation. The only information for every loci is if it originated in population on one or the other side of the hybrid zone (population A or B). All details can be found in [wiki](https://github.com/KamilSJaron/Conjunction/wiki#principles).\n\nIf there is anything unclear or you encounter a bug, please open an issue!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkamilsjaron%2Fconjunction","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkamilsjaron%2Fconjunction","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkamilsjaron%2Fconjunction/lists"}