{"id":18189950,"url":"https://github.com/kullrich/dagchainer","last_synced_at":"2026-01-19T22:32:12.499Z","repository":{"id":86806738,"uuid":"311381533","full_name":"kullrich/dagchainer","owner":"kullrich","description":"Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer","archived":false,"fork":false,"pushed_at":"2021-06-10T20:29:02.000Z","size":4965,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-07T14:51:16.792Z","etag":null,"topics":["dagchainer"],"latest_commit_sha":null,"homepage":"","language":"Roff","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/kullrich.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":"2020-11-09T15:27:08.000Z","updated_at":"2022-11-27T18:28:18.000Z","dependencies_parsed_at":"2023-07-12T10:00:32.747Z","dependency_job_id":null,"html_url":"https://github.com/kullrich/dagchainer","commit_stats":{"total_commits":14,"total_committers":1,"mean_commits":14.0,"dds":0.0,"last_synced_commit":"dbf9f2face659794ee5ceaa560356f81c137fef9"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/kullrich/dagchainer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fdagchainer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fdagchainer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fdagchainer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fdagchainer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kullrich","download_url":"https://codeload.github.com/kullrich/dagchainer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fdagchainer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28587241,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T20:45:59.482Z","status":"ssl_error","status_checked_at":"2026-01-19T20:45:41.500Z","response_time":67,"last_error":"SSL_read: 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":["dagchainer"],"created_at":"2024-11-03T04:04:39.895Z","updated_at":"2026-01-19T22:32:12.477Z","avatar_url":"https://github.com/kullrich.png","language":"Roff","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4273760.svg)](https://doi.org/10.5281/zenodo.4273760)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/dagchainer/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/dagchainer/badges/downloads.svg)](https://anaconda.org/bioconda/dagchainer)\n\n# dagchainer\nFork of the DAGchainer project https://sourceforge.net/projects/dagchainer\n\nDAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).\n\nOriginal Project Admins:\n\n[Joshua Orvis](https://sourceforge.net/u/jorvis/)\n\n[Brian Haas](https://sourceforge.net/u/bhaas/)\n\nOriginal Project Page:\n\n[http://dagchainer.sourceforge.net/](http://dagchainer.sourceforge.net/)\n\n- only minor changes made to compile on macOS\n\n# Building DAGchainer\n\n```\ngit clone https://github.com/kullrich/dagchainer.git\nexport PREFIX=\".\"\ncd dagchainer;make clean;make\n```\n\n# Building DAGchainer - Bioconda\n\n```\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\n\nconda install dagchainer\n```\n\n# Run DAGchainer\n\n```\n./dagchainer/bin/run_DAG_chainer.pl\n```\n\n# Run Java_XY_plotter\n\n```\n./dagchainer/src/Java_XY_plotter/run_XYplot.pl ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered\n```\n\n# Example\n\n```\n./dagchainer/bin/run_DAG_chainer.pl -i ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered -s -I\nless ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered.aligncoords\n```\n\n# Manual\n\nsee manual and further options here [http://dagchainer.sourceforge.net/](http://dagchainer.sourceforge.net/)\n\n# References\n\nHaas B. J., Delcher A. L., Wortman J. R., and Salzberg S. L. (2004). **DAGchainer: a tool for mining segmental genome duplications and synteny.** *Bioinformatics*, **20(18)**, 3643-3646. [https://doi.org/10.1093/bioinformatics/bth397](https://doi.org/10.1093/bioinformatics/bth397)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fdagchainer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkullrich%2Fdagchainer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fdagchainer/lists"}