{"id":27646759,"url":"https://github.com/maxbiostat/deeproot","last_synced_at":"2025-10-09T18:34:26.296Z","repository":{"id":70273532,"uuid":"51942077","full_name":"maxbiostat/DeepRoot","owner":"maxbiostat","description":"scripts for a simulation study in (bielejec et al 2014)","archived":false,"fork":false,"pushed_at":"2017-03-03T11:32:22.000Z","size":13,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-24T01:41:44.464Z","etag":null,"topics":["paper","sequence-simulator"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":false,"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/maxbiostat.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,"zenodo":null}},"created_at":"2016-02-17T17:42:28.000Z","updated_at":"2018-10-22T18:30:09.000Z","dependencies_parsed_at":"2023-02-22T03:46:19.124Z","dependency_job_id":null,"html_url":"https://github.com/maxbiostat/DeepRoot","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/maxbiostat/DeepRoot","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxbiostat%2FDeepRoot","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxbiostat%2FDeepRoot/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxbiostat%2FDeepRoot/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxbiostat%2FDeepRoot/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/maxbiostat","download_url":"https://codeload.github.com/maxbiostat/DeepRoot/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxbiostat%2FDeepRoot/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279001916,"owners_count":26083226,"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":"2025-10-09T02:00:07.460Z","response_time":59,"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":["paper","sequence-simulator"],"created_at":"2025-04-24T01:23:30.124Z","updated_at":"2025-10-09T18:34:26.291Z","avatar_url":"https://github.com/maxbiostat.png","language":"Shell","readme":"#### .:Scripts for a simulation study used in [Bielejec et al. (2014)](http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-133):\n\n**DEPENDENCIES**\n- compiled BEAST jar with PIBUSS core and parsers enabled.\n\n**USAGE**\n\nThere are two scripts. One is set up for a desktop type of workstation, second will run on a PBS/TORQUE cluster.\nAdjust the simulation settings and paths and simply do:\n\n\u003e ./run_deep_root\n\nor reserve your time on the cluster and do:\n\n\u003e ./run_deep_root.pbs\n\nThere is also an R script for analysis the output.\n\n**LICENSE**\n\n  \"THE BEER-WARE LICENSE\" (Revision 42):\n  \u003cfilip.bielejec(sorry_spybots)rega.kuleuve.be\u003e wrote this software. As long as you retain this notice you\n  can do whatever you want with this stuff. If we meet some day, and you think\n  this stuff is worth it, you can buy me a beer in return. Filip Bielejec\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxbiostat%2Fdeeproot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxbiostat%2Fdeeproot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxbiostat%2Fdeeproot/lists"}