{"id":18621313,"url":"https://github.com/4ment/sts-test","last_synced_at":"2025-11-03T13:30:29.360Z","repository":{"id":92150296,"uuid":"136397223","full_name":"4ment/sts-test","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2018-06-08T09:09:15.000Z","size":9286,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-27T04:42:25.953Z","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/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":"2018-06-06T23:39:53.000Z","updated_at":"2018-06-08T09:09:16.000Z","dependencies_parsed_at":null,"dependency_job_id":"14d6f148-3abc-433d-b664-5457eeee9299","html_url":"https://github.com/4ment/sts-test","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fsts-test","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fsts-test/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fsts-test/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fsts-test/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/sts-test/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239414682,"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":[],"created_at":"2024-11-07T04:10:30.458Z","updated_at":"2025-11-03T13:30:29.321Z","avatar_url":"https://github.com/4ment.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"Sequential Tree Sampler (STS)\n=============================\n\nThe sequential tree sampler implements a prototype of online phylogenetics, updating a posterior distribution generated by MrBayes with new sequences.\nThe algorithm has been described and its performance evaluated in [a manuscript][preprint].\nThe scripts used to generate the figures can be found [here](https://github.com/OnlinePhylo/sts-online-experiments).\n\n## Dependencies\n\n* [smctc][smctc] - included as git submodule (`git submodule update --init`)\n* [lcfit][lcfit] - included as git submodule (`git submodule update --init`)\n* [Bio++ version 2.2.0][bpp] `core`, `seq`, and `phyl` modules. Note that debian \u0026 ubuntu up to 16.04 include v2.1.0 which is too old. Bio++ should be installed from source using the `bpp-setup.sh` script on these systems.\n* [cmake][cmake]\n* [gsl version 1.16][gsl] Note that gsl v2 is not currently supported.\n* [nlopt][nlopt]\n* [beagle][beagle] version 2.1 (Optional)\n* [google test][gtest] this is libgtest on debian/ubuntu (Optional)\n\n## Compiling\n\n1. Install dependencies\n2. run `make`\n\nBinaries will be build in `_build/release`\n\n## Adding taxa to an existing posterior\n\nThe tool `sts-online` adds taxa to an existing posterior tree sample.\n`sts-online` operates on a fasta file and tree file in nexus format.\nThe fasta file must contain an alignment with a superset of the taxa in the tree file.\n\nCurrently only the Jukes-Cantor model is supported.\n\n### Example invocation\n\n    sts-online -b 250 -p 2 --proposal-method lcfit 10taxon-01.fasta 10tax_trim_t1.t 10tax_trim_t1.sts.json\n\nIn this example, we use an alignment containing 10 sequences and a posterior sample of trees generated by MrBayes with an alignment that does not contain the sequence labeled `t1`.\n`sts-online` ignores the first 250 trees from `50tax_trim.run1.t` and  uses a particle factor of 2. The `10tax_trim_t1.sts.json` file will contain the updated trees.\n\n\n\n[preprint]: http://biorxiv.org/content/early/2017/06/02/145219\n[smctc]: http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/johansen/smctc/\n[lcfit]: http://github.com/matsengrp/lcfit/\n[beagle]: https://code.google.com/p/beagle-lib/\n[bpp]: http://biopp.univ-montp2.fr/\n[cmake]: http://www.cmake.org/\n[gsl]: https://www.gnu.org/software/gsl/\n[nlopt]: http://ab-initio.mit.edu/wiki/index.php/NLopt\n[gtest]: https://github.com/google/googletest\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fsts-test","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Fsts-test","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fsts-test/lists"}