{"id":356517,"url":"https://github.com/palaeoware/trevosim/","last_synced_at":"2026-08-22T06:41:41.389Z","repository":{"id":112069926,"uuid":"131329387","full_name":"palaeoware/trevosim","owner":"palaeoware","description":"TREvoSim - The [Tr]ee [Evo]lutionary [Sim]ulator program","archived":false,"fork":false,"pushed_at":"2026-07-03T14:33:45.000Z","size":32740,"stargazers_count":7,"open_issues_count":14,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2026-07-30T15:07:59.860Z","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/palaeoware.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":"citation.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2018-04-27T18:03:14.000Z","updated_at":"2026-07-03T14:33:49.000Z","dependencies_parsed_at":"2024-12-13T16:51:34.653Z","dependency_job_id":"8eeb8ea1-7b46-4162-a1ff-0f1be8009a59","html_url":"https://github.com/palaeoware/trevosim","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/palaeoware/trevosim","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/palaeoware","download_url":"https://codeload.github.com/palaeoware/trevosim/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":36321573,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-07-20T02:08:10.276Z","status":"online","status_checked_at":"2026-08-05T02:00:06.619Z","response_time":104,"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"}},"owner":{"login":"palaeoware","name":"palaeoware","uuid":"38782482","kind":"organization","description":"Palaeontology Software for People Stuck in the Past","email":"palaeoware@gmail.com","website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/38782482?v=4","repositories_count":1,"last_synced_at":"2023-03-05T12:28:00.975Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/palaeoware","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-03-05T12:28:00.975Z","updated_at":"2023-03-05T12:28:00.975Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/palaeoware","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/palaeoware/repositories"},"packages":[],"commits":{"id":9624762,"full_name":"palaeoware/trevosim","default_branch":"master","total_commits":510,"total_committers":3,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":170.0,"dds":0.08431372549019611,"past_year_total_commits":99,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":49.5,"past_year_dds":0.02020202020202022,"last_synced_at":"2026-08-20T05:32:56.521Z","last_synced_commit":"7c64bb84f383715622f9fd574e4373f745271275","created_at":"2025-04-11T10:45:02.427Z","updated_at":"2026-08-20T05:32:55.804Z","committers":[{"name":"RussellGarwood","email":"russell.garwood@manchester.ac.uk","login":"RussellGarwood","count":467},{"name":"Alan R.T. Spencer","email":"alan.spencer@imperial.ac.uk","login":"alanspencer","count":31},{"name":"Martin R. Smith","email":"1695515+ms609","login":"ms609","count":12}],"past_year_committers":[{"name":"RussellGarwood","email":"russell.garwood@manchester.ac.uk","login":"RussellGarwood","count":97},{"name":"Alan R.T. Spencer","email":"alan.spencer@imperial.ac.uk","login":"alanspencer","count":2}],"commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2026-08-21T00:00:17.498Z","repositories_count":6767512,"commits_count":980840375,"contributors_count":41353310,"owners_count":1362607,"committers_count":3357028,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues":{"table":{"full_name":"palaeoware/trevosim","html_url":"https://github.com/palaeoware/trevosim","last_synced_at":"2026-08-21T06:06:15.913Z","status":null,"issues_count":63,"pull_requests_count":29,"avg_time_to_close_issue":3347107.659574468,"avg_time_to_close_pull_request":620824.0,"issues_closed_count":47,"pull_requests_closed_count":22,"pull_request_authors_count":2,"issue_authors_count":4,"avg_comments_per_issue":1.8412698412698414,"avg_comments_per_pull_request":0.5172413793103449,"merged_pull_requests_count":16,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":5,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":12869305.0,"past_year_avg_time_to_close_pull_request":17.0,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":0.2,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":1,"created_at":"2025-04-11T10:45:03.607Z","updated_at":"2026-08-21T06:06:15.913Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/palaeoware%2Ftrevosim/issues","issue_labels_count":{"table":{"enhancement":8,"documentation":3,"bug":3}},"pull_request_labels_count":{"table":{}},"issue_author_associations_count":{"table":{"CONTRIBUTOR":59,"NONE":4}},"pull_request_author_associations_count":{"table":{"CONTRIBUTOR":28,"NONE":1}},"issue_authors":{"table":{"ms609":49,"RussellGarwood":11,"atcribb":2,"alanspencer":1}},"pull_request_authors":{"table":{"ms609":21,"RussellGarwood":8}},"host":{"table":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2026-08-22T00:00:08.916Z","repositories_count":16225730,"issues_count":41906340,"pull_requests_count":133575862,"authors_count":11492864,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"}},"past_year_issue_labels_count":{"table":{"enhancement":3,"bug":1}},"past_year_pull_request_labels_count":{"table":{}},"past_year_issue_author_associations_count":{"table":{"CONTRIBUTOR":5}},"past_year_pull_request_author_associations_count":{"table":{"CONTRIBUTOR":1}},"past_year_issue_authors":{"table":{"RussellGarwood":5}},"past_year_pull_request_authors":{"table":{"RussellGarwood":1}},"maintainers":[],"active_maintainers":[]}},"events":{"total":{"DeleteEvent":5,"PullRequestEvent":7,"IssuesEvent":5,"WatchEvent":1,"IssueCommentEvent":17,"PushEvent":86,"CreateEvent":7},"last_year":{"PushEvent":28}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"docs_build/_sources/requirementsinstallation.rst.txt","sha":null,"kind":"manifest","created_at":"2024-06-11T16:26:00.578Z","updated_at":"2024-06-11T16:26:00.578Z","repository_link":"https://github.com/palaeoware/trevosim/blob/master/docs_build/_sources/requirementsinstallation.rst.txt","dependencies":[{"id":18544825294,"package_name":"RequirementsandInstallationfromBinaries","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825295,"package_name":"Requirements","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825296,"package_name":"TREvoSimhasnominimumrequirementsassuch","ecosystem":"pypi","requirements":",andwillrunonmoststandardsystems","direct":true,"kind":"runtime","optional":false},{"id":18544825297,"package_name":"InstallationfromBinaries","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825298,"package_name":"Binarydownloadlocations","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825299,"package_name":"Youcandownloadpre-compiledbinaryreleasesandpackagedinstallersfromtheTREvoSimGitHubrepository","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825300,"package_name":"Windows64-bit","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825301,"package_name":"ForWindowsusersweprovidetwomeansofinstallation","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825302,"package_name":"1.Aportablebinaryreleasewithina.ZIParchive.Torunthis","ecosystem":"pypi","requirements":",allyouneedtodoisextracttheziptoaconvenientlocation,anddoubleclickonthe.exefile.","direct":true,"kind":"runtime","optional":false},{"id":18544825303,"package_name":"2.Aselfcontainedinstaller-downloadanddoubleclickonthefile","ecosystem":"pypi","requirements":",whichwillguideyouthoughtheinstallationprocess.","direct":true,"kind":"runtime","optional":false},{"id":18544825304,"package_name":"MacOS","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825305,"package_name":"ForTREvoSimv1.Xandv2.Xweprovidea.ZIParchivecontainingtheTREvoSimprogramthatcanbedownloadedfromtheTREvoSimGitHubrepository.","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825306,"package_name":"ForTREvoSimv3.Xweprovidea.DMGimagetoinstallthesoftware.Downloadanddoubleclickonthe.dmgandfollowtheonscreeninstructions.Youmayberequiredtotheapprovethesoftwareinsecurityandprivacysettingsbeforeitwilllaunch.","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825307,"package_name":"Note","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825308,"package_name":"Ubuntu64-bit","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825309,"package_name":"ForLinuxusers","ecosystem":"pypi","requirements":",pleaseseethe","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2024-06-11T16:26:01.817Z","updated_at":"2024-06-11T16:26:01.817Z","repository_link":"https://github.com/palaeoware/trevosim/blob/master/requirements.txt","dependencies":[{"id":18544825310,"package_name":"sphinx","ecosystem":"pypi","requirements":"==5.3.0","direct":true,"kind":"runtime","optional":false},{"id":18544825311,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"==1.1.1","direct":true,"kind":"runtime","optional":false},{"id":18544825312,"package_name":"sphinx-multiproject","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18544825313,"package_name":"readthedocs-sphinx-search","ecosystem":"pypi","requirements":"==0.3.2","direct":true,"kind":"runtime","optional":false}]}],"score":4.143134726391533,"created_at":"2025-04-11T10:17:17.245Z","updated_at":"2026-08-22T06:41:41.389Z","avatar_url":"https://github.com/palaeoware.png","language":"C++","codemeta":{"@context":"https://w3id.org/codemeta/3.0","type":"SoftwareSourceCode","applicationCategory":"Evolutionary simulation","author":[{"id":"https://orcid.org/0000-0002-2803-9471","type":"Person","affiliation":{"type":"Organization","name":"Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom; Natural History Museum, London, SW7 5BD, United Kingdom"},"email":"russell.garwood@gmail.com","familyName":"Garwood","givenName":"Russell J."},{"type":"Role","schema:author":"https://orcid.org/0000-0002-2803-9471","roleName":"Developer","startDate":"2017-01-01"},{"id":"https://orcid.org/0000-0001-6590-405X","type":"Person","affiliation":{"type":"Organization","name":"Department of Earth Science and Engineering, Imperial College, London, SW7 2AZ, United Kingdom; Natural History Museum, London, SW7 5BD, United Kingdom"},"familyName":"Spencer","givenName":"Alan R.T. "},{"type":"Role","schema:author":"https://orcid.org/0000-0001-6590-405X","roleName":"Developer","startDate":"2019-07-01"}],"codeRepository":"git+https://github.com/palaeoware/trevosim","dateModified":"2024-08-22","datePublished":"2021-01-21","description":"TREvoSim is an individual-based evolutionary simulation. It creates evolutionary trees and associated character data using a model that with a fitness algorithm and replication that incorporates mutation.","downloadUrl":"https://github.com/palaeoware/trevosim/releases/tag/v3.0.0","identifier":"10.5281/zenodo.13358420","keywords":["Phylogenetics","evolution","modelling"],"license":"https://spdx.org/licenses/GPL-3.0","name":"TREvoSim","operatingSystem":["Windows","MacOS","Linux"],"programmingLanguage":"C++","releaseNotes":"The changes in v3.0.0 are described and discussed fully in the associated paper. In brief, these include:\n\n-- New character options\n-- New default simulation parameters\n-- Ecosystem engineering functionality\n-- An expanding playing field mode\n-- New logging capabilities\n-- The option to match fitness peaks across environments\n-- A no selection mode\n-- Mixing of organisms between playing fields\n-- Perturbations (periods of accelerated environmental change)\n-- The ability to run the simulation for a user-defined number of iterations, as opposed to for set number of species\n-- Abstraction of the fitness algorithm from the genome via many-to-one mapping (stochastic layer)\n-- A test suite integrated into the software build","review":{"type":"Review","reviewAspect":"TREvoSim v3: An individual based simulation for generating trees and character data","reviewBody":"Paper accompanying release of v3.0.0"},"version":"3.0.0","developmentStatus":"active","funding":" BBSRC - BB/N015827/1, NERC - NE/T000813/1, Leverhulme Trust -  RPG-2023-234, the Alexander von Humboldt Foundation","issueTracker":"https://github.com/palaeoware/trevosim/issues","referencePublication":"https://doi.org/10.21105/joss.06722"},"publiccode":null,"project_url":"https://summary.ecosyste.ms/api/v1/projects/356517","html_url":"https://summary.ecosyste.ms/projects/356517"}