{"id":18621310,"url":"https://github.com/4ment/torchtree-bito","last_synced_at":"2025-11-03T13:30:29.006Z","repository":{"id":92150306,"uuid":"419913929","full_name":"4ment/torchtree-bito","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2023-08-23T02:56:40.000Z","size":68,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-12-27T04:42:26.061Z","etag":null,"topics":["beagle","bito","phylogenetics","pybind11","python","torchtree"],"latest_commit_sha":null,"homepage":"","language":"Python","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/4ment.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2021-10-22T00:12:00.000Z","updated_at":"2022-09-01T03:50:13.000Z","dependencies_parsed_at":null,"dependency_job_id":"3d77de76-5ec3-46d0-bcb4-8f1fe3816343","html_url":"https://github.com/4ment/torchtree-bito","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%2Ftorchtree-bito","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-bito/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-bito/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-bito/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/torchtree-bito/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239414686,"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":["beagle","bito","phylogenetics","pybind11","python","torchtree"],"created_at":"2024-11-07T04:10:29.266Z","updated_at":"2025-11-03T13:30:28.948Z","avatar_url":"https://github.com/4ment.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# torchtree-bito\n\ntorchtree-bito is a package providing an interface to [BITO] for [torchtree]\n\n## Dependencies\n - [torchtree]\n - [BITO]\n\n## Installation\n\nInstructions about installing BITO can be found on the [BITO] website.\n\n### Get the source code\n```bash\ngit clone https://github.com/4ment/torchtree-bito\ncd torchtree-bito\n```\n\n### Install using pip\n```bash\npip install .\n```\n\n## Check install\n```bash\npython -c \"import bito\"\n```\n\n```bash\ntorchtree --help\n```\n\n## Command line arguments\nThe torchtree-bito plugin adds these arguments to the torchtree CLI:\n\n```bash\ntorchtree-cli advi --help\n  ...\n  --bito                use bito\n  --bito_gpu            use GPU in bito/BEAGLE\n  --bito_disable_sse    disable SSE in bito/BEAGLE\n```\n\n## Quick start\ntorchtree will approximate the posterior distribution of an unrooted tree with an HKY substitution model using variational \n```bash\ntorchtree examples/advi/fluA-HKY.json\n```\n\nThe JSON file can be generated by providing an alignment and a tree to the torchtree CLI:\n```bash\ntorchtree-cli advi -i foo.fa -t foo.tree -m HKY --bito \u003e foo.json\n```\n\n[torchtree]: https://github.com/4ment/torchtree\n[BITO]: https://github.com/phylovi/bito","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-bito","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Ftorchtree-bito","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-bito/lists"}