{"id":18189937,"url":"https://github.com/kullrich/kakscalculator2","last_synced_at":"2026-03-07T16:03:39.392Z","repository":{"id":86806785,"uuid":"312365517","full_name":"kullrich/kakscalculator2","owner":"kullrich","description":"Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2","archived":false,"fork":false,"pushed_at":"2023-05-18T09:37:22.000Z","size":2033,"stargazers_count":13,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-01T21:50:06.292Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/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}},"created_at":"2020-11-12T18:41:41.000Z","updated_at":"2025-05-01T09:29:38.000Z","dependencies_parsed_at":"2023-07-12T10:00:42.436Z","dependency_job_id":null,"html_url":"https://github.com/kullrich/kakscalculator2","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/kullrich/kakscalculator2","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fkakscalculator2","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fkakscalculator2/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fkakscalculator2/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fkakscalculator2/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kullrich","download_url":"https://codeload.github.com/kullrich/kakscalculator2/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fkakscalculator2/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30221193,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-07T14:02:48.375Z","status":"ssl_error","status_checked_at":"2026-03-07T14:02:43.192Z","response_time":53,"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":[],"created_at":"2024-11-03T04:04:37.274Z","updated_at":"2026-03-07T16:03:39.374Z","avatar_url":"https://github.com/kullrich.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4273737.svg)](https://doi.org/10.5281/zenodo.4273737)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/kakscalculator2/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/kakscalculator2/badges/downloads.svg)](https://anaconda.org/bioconda/kakscalculator2)\n\n# kakscalculator2\nFork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2\n\nThis software is a toolkit of incorporating gamma series methods and sliding window strategies.\n\nOriginal Project Admins:\n\n[Dapeng Wang](https://sourceforge.net/u/wangdp/)\n\nOriginal Project Page:\n\n[https://sourceforge.net/projects/kakscalculator2/](https://sourceforge.net/projects/kakscalculator2/)\n\n- only minor changes made to compile on macOS\n\n# Building KaKs_Calculator2.0\n\n```\ngit clone https://github.com/kullrich/kakscalculator2.git\nexport PREFIX=\".\"\ncd kakscalculator2;make clean;make\n```\n\n# Building KaKs_Calculator2.0 - Bioconda\n\n```\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\n\nconda install kakscalculator2\n```\n\n# Run KaKs_Calculator2.0\n\n```\n./kakscalculator2/bin/KaKs_Calculator -h\n```\n\n# Example\n\n```\n./bin/KaKs_Calculator -i ./examples/example.axt -o ./examples/example.axt.kaks -m YN\n```\n\n# Manual\n\n```\n./kakscalculator2/bin/KaKs_Calculator -h\n```\n\nsee manual in KaKs_Calculator2.0.tar.gz /doc/KaKs_Calculator2.0_manual.pdf from [https://sourceforge.net/projects/kakscalculator2/](https://sourceforge.net/projects/kakscalculator2/)\n\n# References\n\nWang D., Wan H-L., Zhang S., and Yu J. (2009). **γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.** *Biology Direct*, **4(20)**. [https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-20](https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-20)\n\nWang D., Zhang S., He F., Zhu J., Hu S., Yu J. (2009). **How Do Variable Substitution Rates Influence Ka and Ks Calculations?** *Genomics Proteomics Bioinformatics*, **7(3)**, 116-127. [https://dx.doi.org/10.1016/S1672-0229(08)60040-6](https://dx.doi.org/10.1016/S1672-0229(08)60040-6)\n\nWang D., Zhang Y., Zhang Z., Zhu J., Yu J. (2010). **KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.** *Genomics Proteomics Bioinformatics*, **8(1)**, 77-80. [https://dx.doi.org/10.1016/S1672-0229(10)60008-3](https://dx.doi.org/10.1016/S1672-0229(10)60008-3)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fkakscalculator2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkullrich%2Fkakscalculator2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkullrich%2Fkakscalculator2/lists"}