{"id":43849050,"url":"https://github.com/alberdilab/ehi_prokaryote_diversification","last_synced_at":"2026-02-06T06:14:46.655Z","repository":{"id":209451868,"uuid":"724043340","full_name":"alberdilab/ehi_prokaryote_diversification","owner":"alberdilab","description":"Data and code repository for the prokaryote diversification study based on EHI data","archived":false,"fork":false,"pushed_at":"2024-03-19T16:04:46.000Z","size":27735,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-22T08:56:50.225Z","etag":null,"topics":["project"],"latest_commit_sha":null,"homepage":null,"language":"R","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/alberdilab.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}},"created_at":"2023-11-27T09:28:59.000Z","updated_at":"2024-02-08T09:27:23.000Z","dependencies_parsed_at":"2023-12-15T11:38:52.984Z","dependency_job_id":null,"html_url":"https://github.com/alberdilab/ehi_prokaryote_diversification","commit_stats":null,"previous_names":["alberdilab/ehi_prokaryote_diversification"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/alberdilab/ehi_prokaryote_diversification","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alberdilab%2Fehi_prokaryote_diversification","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alberdilab%2Fehi_prokaryote_diversification/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alberdilab%2Fehi_prokaryote_diversification/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alberdilab%2Fehi_prokaryote_diversification/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alberdilab","download_url":"https://codeload.github.com/alberdilab/ehi_prokaryote_diversification/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alberdilab%2Fehi_prokaryote_diversification/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29153396,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T02:39:25.012Z","status":"ssl_error","status_checked_at":"2026-02-06T02:37:22.784Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":["project"],"created_at":"2026-02-06T06:14:45.955Z","updated_at":"2026-02-06T06:14:46.646Z","avatar_url":"https://github.com/alberdilab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# EHI - Host-shaped prokaryote diversification\nData and code repository for the prokaryote diversification study based on EHI data.\n\n## 1 - Phylogenetic clusters\nIn this initial step the phylogeny of EHI MAGs is split into phylogenetically related clusters of MAGs. Clusters are generated at different thresholds of phylogenetic distances: 0.3, 0.35, 0.4 and 0.45.\n\n- **Code:** 1-phylogenetic_clusters.Rmd\n- **Output at 0.30:** results/cluster_table_30.Rdata\n- **Output at 0.35:** results/cluster_table_35.Rdata\n- **Output at 0.40:** results/cluster_table_40.Rdata\n- **Output at 0.45:** results/cluster_table_45.Rdata\n\nDiverse clusters are defined as those containing \u003e10 MAGs.\n\n| Distance threshold | Total clusters | Diverse clusters | Mean MAGs | Max MAGs | Mean hosts | Max hosts |\n|---|---|---|---|---|---|---|\n| 0.30 | 2680 | 141 | 4.20 | 235 | 1.96 | 34 |\n| 0.35 | 2193 | 158 | 5.21 | 441 | 2.17 | 34 |\n| 0.40 | 1836 | 170 | 6.32 | 442 | 2.39 | 34 |\n| 0.45 | 1557 | 167 | 7.56 | 442 | 2.63 | 37 |\n\n- **Total clusters:** number of clusters with at least 1 EHI MAG\n- **Diverse clusters:** number of clusters with \u003e10 MAGs and \u003e5 hosts.\n- **Mean MAGs:** average number of MAGs per cluster\n- **Max MAGs:** maximum number of MAGs per cluster\n- **Mean hosts:** average number of hosts per cluster\n- **Max hosts:** maximum number of hosts per cluster\n\n## 2 - Cluster analysis\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falberdilab%2Fehi_prokaryote_diversification","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falberdilab%2Fehi_prokaryote_diversification","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falberdilab%2Fehi_prokaryote_diversification/lists"}