{"id":18818521,"url":"https://github.com/smithsonian/fabaceae_phylogenomics_workflow","last_synced_at":"2026-02-07T14:02:36.374Z","repository":{"id":142086281,"uuid":"100393188","full_name":"Smithsonian/Fabaceae_Phylogenomics_workflow","owner":"Smithsonian","description":"Target-enrichment data processing in legumes","archived":false,"fork":false,"pushed_at":"2023-06-11T13:31:31.000Z","size":802,"stargazers_count":6,"open_issues_count":0,"forks_count":2,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-07-21T15:44:43.694Z","etag":null,"topics":["legumes","molecular-evolution","phylogenetics","target-enrichment"],"latest_commit_sha":null,"homepage":"","language":null,"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/Smithsonian.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,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-08-15T15:44:42.000Z","updated_at":"2025-07-16T06:53:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"adb338a6-28a9-4a61-b874-6c161177a1e3","html_url":"https://github.com/Smithsonian/Fabaceae_Phylogenomics_workflow","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Smithsonian/Fabaceae_Phylogenomics_workflow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Smithsonian%2FFabaceae_Phylogenomics_workflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Smithsonian%2FFabaceae_Phylogenomics_workflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Smithsonian%2FFabaceae_Phylogenomics_workflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Smithsonian%2FFabaceae_Phylogenomics_workflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Smithsonian","download_url":"https://codeload.github.com/Smithsonian/Fabaceae_Phylogenomics_workflow/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Smithsonian%2FFabaceae_Phylogenomics_workflow/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29196625,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-07T12:38:28.597Z","status":"ssl_error","status_checked_at":"2026-02-07T12:38:23.888Z","response_time":63,"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":["legumes","molecular-evolution","phylogenetics","target-enrichment"],"created_at":"2024-11-08T00:17:06.706Z","updated_at":"2026-02-07T14:02:36.369Z","avatar_url":"https://github.com/Smithsonian.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Fabaceae phylogenomics workflow\nThis repository contains instructions on handling target-enrichment (bait-capture) data using [HybPiper](https://github.com/mossmatters/HybPiper) and performing subsequent phylogenetic analyses on the Smithsonian Institution HPC (Hydra cluster). If you don't have your own dataset, you can use tutorial data from [here](https://github.com/mossmatters/HybPiper/tree/master/test_dataset). If you don't have access to the cluster, install all [dependencies](https://github.com/mossmatters/HybPiper#dependencies) and programs used here such as MAFFT, TrimAl, RAxML on your system and run the main commands from the job files. Follow steps in the [Data_processing.md](https://github.com/Smithsonian/Fabaceae_Phylogenomics_workflow/blob/master/Data_processing.md).\n\n\nPaper:\n\nVatanparast, M., A. Powell, J. J. Doyle, and A. N. Egan. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. [Applications in Plant Sciences 6(3): e01036](https://onlinelibrary.wiley.com/doi/full/10.1002/aps3.1036)\n\nDatasets are available from Figshare: https://doi.org/10.6084/m9.figshare.c.4040372.v4\n\n\nExample phylogenetic trees using different species tree reconstruction methods.\n\n![example-tree](https://user-images.githubusercontent.com/13125143/35277516-f3342a4e-003e-11e8-8fa7-9bb5c513a2b0.jpg)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithsonian%2Ffabaceae_phylogenomics_workflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithsonian%2Ffabaceae_phylogenomics_workflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithsonian%2Ffabaceae_phylogenomics_workflow/lists"}