{"id":50718674,"url":"https://github.com/husonlab/trees-to-networks-tutorial","last_synced_at":"2026-06-09T21:30:46.425Z","repository":{"id":360681543,"uuid":"1243390485","full_name":"husonlab/trees-to-networks-tutorial","owner":"husonlab","description":null,"archived":false,"fork":false,"pushed_at":"2026-05-27T12:26:23.000Z","size":22210,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-27T13:21:43.286Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/husonlab.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-05-19T09:48:03.000Z","updated_at":"2026-05-27T12:28:07.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/husonlab/trees-to-networks-tutorial","commit_stats":null,"previous_names":["husonlab/trees-to-networks-tutorial"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/husonlab/trees-to-networks-tutorial","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/husonlab%2Ftrees-to-networks-tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/husonlab%2Ftrees-to-networks-tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/husonlab%2Ftrees-to-networks-tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/husonlab%2Ftrees-to-networks-tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/husonlab","download_url":"https://codeload.github.com/husonlab/trees-to-networks-tutorial/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/husonlab%2Ftrees-to-networks-tutorial/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34127342,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-09T02:00:06.510Z","response_time":63,"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":[],"created_at":"2026-06-09T21:30:45.801Z","updated_at":"2026-06-09T21:30:46.419Z","avatar_url":"https://github.com/husonlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003e [!WARNING]\n\u003e **This repository is under active development for ISMB 2026.**\n\u003e\n\u003e Tutorial: **From Trees to Networks**, scheduled for July-12, 9am-1pm at ISMB 2026.\n\u003e\n\u003e Materials will be finalized by **June 16, 2026**. Until then, files may\n\u003e change without notice and some sections may be incomplete. If you're a\n\u003e registered attendee, please follow [`SETUP.md`](SETUP.md) starting one\n\u003e week before the tutorial.\n\n# From Trees to Networks\n\nTutorial materials for *From Trees to Networks*, originally developed for the\n[ISMB 2026](https://www.iscb.org/ismb2026/) tutorial program [(tutorial IP3)](https://www.iscb.org/ismb2026/whats-happening/tutorials#ip3). The tutorial\ncovers phylogenetic and phylogenomic analysis using gene trees, species trees,\nand phylogenetic networks, with hands-on exercises using the *Anopheles\ngambiae* species complex from [Fontaine et al. (2015)](https://www.science.org/doi/10.1126/science.1258524) — a textbook dataset\nfor studying pervasive autosomal introgression.\n\n## Tutorial Overview\n\nParticipants will work through a phylogenomic inference pipeline from sequence\nalignments to phylogenetic networks:\n\n- **Part I — Trees** (110 min): per-locus gene tree inference with\n  maximum likelihood (IQ-TREE 3) and Bayesian inference (BEAST X), then\n  coalescent species-tree estimation with wASTRAL (ASTER)\n- **Part II — Networks** (110 min): visualizing conflicting phylogenetic\n  signal with SplitsTree, building networks interactively with PhyloSketch,\n  and inferring networks from gene tree sets with PhyloCompare.\n\nThe pedagogical core: when the genome has been pervasively introgressed,\ntrees and tree-summary methods can return confident but biologically\nincorrect answers. Networks make the conflict visible rather than\naveraging it away.\n\n## Audience\n\nThe tutorial is aimed at researchers with some prior exposure to\nphylogenetics. Familiarity with command-line tools and basic\nsequence-alignment concepts is assumed. No prior experience with\nphylogenetic networks is required.\n\n## Getting Started\n\n1. Read [`doc/Setup.md`](doc/Setup.md) for installation instructions and prerequisites\n   — **complete this before tutorial day**.\n2. Clone this repository to your laptop:\n   ```bash\n   git clone https://github.com/husonlab/trees-to-networks-tutorial.git\n   ```\n3. On tutorial day, follow the hands-on guide [`doc/Hands-On-Guide.md`](doc/Hands-On-Guide.md).\n\n## Repository Structure\n\n```\ntrees-to-networks-tutorial/\n├── README.md\n├── doc/                    # documents: Setup, Hands-On Guide, Cheat Sheet, References\n├── slides/                 # tutorial slide deck (PDF)\n├── data/                   # 15 per-locus alignments + metadata\n├── data-prep/              # scripts used to build data/ from raw MAF\n├── precomputed/            # expected outputs for every hands-on step\n│   ├── iqtree/             # IQ-TREE gene trees \u0026 NEXUS tree set\n│   ├── astral/             # wASTRAL species tree\n│   ├── beast/              # BEAST X posterior on locus X_dist_04\n│   └── networks/           # SplitsTree \u0026 PhyloFusion network outputs\n└── tools/                  # Additional tools\n```\n\nA guiding principle: **every output participants might generate during the\ntutorial has a precomputed version in `precomputed/`**. If a step fails on\nyour laptop, copy the precomputed file and rejoin at the next step.\n\n## Citation\n\nIf you use these materials, please cite:\n\n\u003e Huson, D.H., Gautam, A., Cetinkaya, B. (2026). *From Trees to Networks.*\n\u003e ISMB 2026 Tutorial. https://github.com/husonlab/trees-to-networks-tutorial\n\nFor the source data:\n\n\u003e Fontaine, M.C., Pease, J.B., Steele, A., et al. (2015). Extensive\n\u003e introgression in a malaria vector species complex revealed by\n\u003e phylogenomics. *Science* 347(6217): 1258524.\n\u003e https://doi.org/10.1126/science.1258524\n\n## License\n\nTutorial materials (slides, exercises, scripts) are released under\n[CC-BY-4.0](LICENSE). Source data are derived from the Fontaine et al. (2015)\nDryad deposit (doi:10.5061/dryad.f4114) and are subject to the terms of that\ndeposit.\n\n## Acknowledgments\n\nThis tutorial would not be possible without the open-source tools developed\nby the phylogenetics community:\n\n- [IQ-TREE](http://www.iqtree.org/) — Minh, Wong, Ly-Trong et al.\n- [BEAST X](https://beast.community) — Baele, Drummond, Suchard, Rambaut, Lemey et al.\n- [ASTRAL](https://github.com/smirarab/ASTRAL) —  Rabiee, Sayyari, and Mirarab\n- [Tracer](https://github.com/beast-dev/tracer) — Rambaut et al.\n- [SplitsTree](https://github.com/husonlab/splitstree6) — Huson lab\n- [PhyloSketch](https://github.com/husonlab/phylosketch2) — Huson lab\n- [PhyloCompare](https://github.com/husonlab/phylocompare) — Huson lab\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhusonlab%2Ftrees-to-networks-tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhusonlab%2Ftrees-to-networks-tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhusonlab%2Ftrees-to-networks-tutorial/lists"}