{"id":22308593,"url":"https://github.com/sysbiochalmers/hgtphylodetect","last_synced_at":"2025-07-29T06:30:45.913Z","repository":{"id":39408820,"uuid":"333121751","full_name":"SysBioChalmers/HGTphyloDetect","owner":"SysBioChalmers","description":"HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.","archived":false,"fork":false,"pushed_at":"2023-02-11T18:59:28.000Z","size":8048,"stargazers_count":36,"open_issues_count":2,"forks_count":5,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-05T08:51:15.511Z","etag":null,"topics":["evolutionary-biology","high-throughput-pipeline","horizontal-gene-transfer","phylogenetics","sequence-analysis","systems-biology"],"latest_commit_sha":null,"homepage":"","language":"Python","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/SysBioChalmers.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-01-26T15:08:12.000Z","updated_at":"2024-12-17T05:50:53.000Z","dependencies_parsed_at":"2023-01-28T23:45:56.619Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/HGTphyloDetect","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/SysBioChalmers/HGTphyloDetect","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FHGTphyloDetect","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FHGTphyloDetect/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FHGTphyloDetect/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FHGTphyloDetect/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/HGTphyloDetect/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FHGTphyloDetect/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267639569,"owners_count":24119780,"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","status":"online","status_checked_at":"2025-07-29T02:00:12.549Z","response_time":2574,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["evolutionary-biology","high-throughput-pipeline","horizontal-gene-transfer","phylogenetics","sequence-analysis","systems-biology"],"created_at":"2024-12-03T20:14:31.747Z","updated_at":"2025-07-29T06:30:44.659Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HGTphyloDetect\nHorizontal gene transfer (HGT) refers to the exchange of genetic material\nbetween disparate groups of organisms other than from parent to offspring,\nwhich has been confirmed as a very significant factor in adaptive\nevolution, disease emergence and metabolic shift that can act across various\nspecies. However, current methods for HGT detection are usually not automatic,\nnarrow applicable or unavailable to use. In this work, we developed a versatile computational\ntoolbox named HGTphyloDetect by combining a high-throughput pipeline together with phylogenetic analysis\nto facilitate comprehensive investigation of the potential mechanism for HGT events. Tests on two case\nstudies suggest that this approach could effectively\nidentify horizontally acquired genes with high accuracy. In-depth phylogenetic analysis further facilitates\nthe navigation of the potential donors and detailed gene transmission process. The HGTphyloDetect toolbox\nis designed for ease of use and could accurately find HGT events with a very low false discovery rate\nin a high-throughput manner.\n\n## HGT identification pipeline\n![image](https://github.com/SysBioChalmers/HGTphyloDetect/blob/master/doc/HGT_pipeline.png)\n\n## Citation\nPlease cite this paper:\nYuan, Le, et al. _HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer._ Briefings in Bioinformatics (2023). https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbad035/7031155.\n\n## Installation\nInstall the latest version with:\n```bash\n$ git clone https://github.com/SysBioChalmers/HGTphyloDetect.git\n$ cd HGTphyloDetect\n$ pip install -r requirements.txt\n```\nPlease note: this is sufficient to run the HGT detection functionality of HGTphyloDetect. Additional software dependencies and installation instructions are specified in the [User tutorial](https://github.com/SysBioChalmers/HGTphyloDetect/blob/master/User%20tutorial.pdf).\n\n## Example\nWe provide a user-friendly example for small test, users just need to prepare a FASTA file including protein id and protein sequence, note that protein id should be from the GenBank protein database.\u003cbr\u003e\u003cbr\u003e\n(1) If you are now in the HGTphyloDetect directory, just enter into the folder [example](https://github.com/SysBioChalmers/HGTphyloDetect/tree/master/example) via the command line:\n```linux\ncd example\n```\n\n(2.1) Then users can run the script for the input file (default AI value = 45, out_pct = 0.90): \n```linux\npython HGT_workflow.py input.fasta\n```\n\n(2.2) If users want to change the default values for the parameters used in the pipeline, e.g., AI value = 40, out_pct = 0.80, just reset the constant values and run the following: \n```linux\npython HGT_workflow.py input.fasta AI=40 out_pct=0.80\n```\n\n(3) Finally, our software could generate the output results as a file under the folder [example](https://github.com/SysBioChalmers/HGTphyloDetect/tree/master/example) for this gene/protein. The output file includes some important information, i.e., Alien index, E value and donor information. For example:\n|Gene/Protein | Alien index | E value | Donor id | \tDonor taxonomy |\n|:---------------:|:---------------:|:---------------:|:---------------:|:---------------:|\n| AAT92670 |   199.18|    3.15e-87|  WP_208929673|  Bacteria/Firmicutes|\n\n## User Manual\nPlease check the documentation [User tutorial](https://github.com/SysBioChalmers/HGTphyloDetect/blob/master/User%20tutorial.pdf) for the user manual. Here you can download this file for your case studies.\n\n## Contact\n* [Le Yuan](https://www.chalmers.se/en/Staff/Pages/leyu.aspx) ([@leyuan](https://github.com/le-yuan)), Chalmers University of Technology, Sweden\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fhgtphylodetect","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fhgtphylodetect","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fhgtphylodetect/lists"}