{"id":18621327,"url":"https://github.com/4ment/aiv-migratory-flyways","last_synced_at":"2025-11-03T13:30:29.381Z","repository":{"id":92149901,"uuid":"68059115","full_name":"4ment/aiv-migratory-flyways","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2017-05-26T10:16:54.000Z","size":3751,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-27T04:42:26.122Z","etag":null,"topics":["data","influenza"],"latest_commit_sha":null,"homepage":null,"language":"Python","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/4ment.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":"2016-09-13T00:27:19.000Z","updated_at":"2022-03-10T09:21:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"1ca32982-1042-4a83-a68f-be2fe60bde6b","html_url":"https://github.com/4ment/aiv-migratory-flyways","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Faiv-migratory-flyways","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Faiv-migratory-flyways/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Faiv-migratory-flyways/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Faiv-migratory-flyways/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/aiv-migratory-flyways/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239414689,"owners_count":19634493,"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","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":["data","influenza"],"created_at":"2024-11-07T04:10:41.434Z","updated_at":"2025-11-03T13:30:29.325Z","avatar_url":"https://github.com/4ment.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America\n\nThis repository contains the data sets supporting the results of the following article:\n\nFourment M, Darling AE, and Holmes EC The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America. _BMC Evolutionary Biology_, 2017, 17:118; DOI: [10.1186/s12862-017-0965-4](http://dx.doi.org/10.1186/s12862-017-0965-4).\n\nData sets are organised by gene (i.e. PB2, PB1, PA, NP, and MP) and each folder contains:\n* a fasta file containing the nucleotide alignment (*-dna.fa)\n* a tree file inferred from the nucleotide alignment (*.tree)\n* a fasta file containing the geographic location of each sequence (*-geo.fa)\n\n\nOther files:\n* *countries.csv* contains the state/province to flyway assignment used in the study.\n\n* *generate-models.py* is a python script that generates command line arguments on the standard output for reproducing the analyses using [_physher_](https://github.com/4ment/physher). For each genes it will generate the command line arguments for:\n  * HRM: homogeneous rate model\n  * 3-TRM: two-rate model with 3 flyways (Pacific, Central/Mississippi, and Atlantic)\n  * 4-TRM: two-rate model with 4 flyways (Pacific, Central, Mississippi, and Atlantic)\n  * 3-FRM: flyway-based model with 3 flyways\n  * 4-FRM: flyway-based model with 4 flyways\n  * Best model found by the genetic algorithm\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Faiv-migratory-flyways","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Faiv-migratory-flyways","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Faiv-migratory-flyways/lists"}