{"id":18538331,"url":"https://github.com/pblischak/hyde","last_synced_at":"2025-04-06T22:10:08.854Z","repository":{"id":57452403,"uuid":"83440527","full_name":"pblischak/HyDe","owner":"pblischak","description":"Hybridization detection using phylogenetic invariants","archived":false,"fork":false,"pushed_at":"2024-10-29T02:09:13.000Z","size":2125,"stargazers_count":46,"open_issues_count":20,"forks_count":14,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-30T17:11:12.507Z","etag":null,"topics":["cython","hybridization","phylogenetic-networks","phylogenomics","python-package"],"latest_commit_sha":null,"homepage":"http://hybridization-detection.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pblischak.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.md","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":"2017-02-28T14:16:17.000Z","updated_at":"2025-02-26T19:07:52.000Z","dependencies_parsed_at":"2022-09-05T17:50:36.847Z","dependency_job_id":"82a67f05-97e7-4460-9dee-803086d7e7db","html_url":"https://github.com/pblischak/HyDe","commit_stats":{"total_commits":177,"total_committers":3,"mean_commits":59.0,"dds":0.480225988700565,"last_synced_commit":"8948a8319c4a84d9997d410d4bc7abf9ca9f383f"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pblischak%2FHyDe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pblischak%2FHyDe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pblischak%2FHyDe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pblischak%2FHyDe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pblischak","download_url":"https://codeload.github.com/pblischak/HyDe/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247557767,"owners_count":20958047,"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":["cython","hybridization","phylogenetic-networks","phylogenomics","python-package"],"created_at":"2024-11-06T19:43:06.359Z","updated_at":"2025-04-06T22:10:08.823Z","avatar_url":"https://github.com/pblischak.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n|Documentation|  |PyPI Badge|\n\nHyDe: Hybridization Detection Using Phylogenetic Invariants\n-----------------------------------------------------------\n\n**Publication:**\n\nBlischak, P. D., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2018.\nHyDe: A Python Package For Genome-Scale Hybridization Detection.\n*Systematic Biology*, doi: `https://doi.org/10.1093/sysbio/syy023 \u003chttps://doi.org/10.1093/sysbio/syy023\u003e`__.\n\n`Read the Docs \u003chttps://hybridization-detection.rtfd.io/\u003e`__\n------------------------------------------------------------\n\nHyDe is a software package that detects hybridization in phylogenomic\ndata sets using phylogenetic invariants. The primary interface for HyDe is a Python\nmodule called ``phyde`` (**P**\\ ythonic **Hy**\\ bridization **De**\\ tection).\n``phyde`` provides a suite of tools for performing hypothesis tests on triples of taxa\nto detect hybridization. To ensure that the necessary\ndependencies for ``phyde`` are available, we suggest using a Python distribution such\nas `Miniconda \u003chttps://conda.io/miniconda.html\u003e`__.\n\nTo facilitate analyses using the Python module, three scripts are provided to\nconduct hybridization detection analyses directly from the command line:\n\n- ``run_hyde.py``: runs a standard hybridization detection analysis on all triples\n  in all directions. Results are also filtered based on whether there is significant\n  evidence for hybridization.\n- ``individual_hyde.py``: tests each individual within a putative hybrid population\n  using a list of specified triples specified.\n- ``bootstrap_hyde.py``: conducts bootstrap resampling of the individuals within\n  the putative hybrid lineages for each specified triple.\n\nThese last two scripts need to be given a three column table of triples\n(P1, Hybrid, P2) that you wish to test:\n\n.. code::\n\n  sp1 sp2 sp3\n  sp1 sp3 sp4\n  sp3 sp4 sp5\n  .\n  .\n  .\n\nYou can also use a results file from a previous analysis as a triples file.\nFor example, you can use the filtered results from the ``run_hyde.py`` script so that\nyou only run analyses on triples that have significant levels of hybridization.\nIf you only have a few hypotheses that you want to test, then you can also pass\na triples file to ``run_hyde.py`` and it will only test those hypotheses rather than\ntesting everything.\n\nMultithreaded versions of these scripts are also available (``run_hyde_mp.py``,\n``individual_hyde_mp.py``, and ``bootstrap_hyde_mp.py``).\nMake sure you have the ``multiprocess`` module installed before you use them.\n\nGraphical User Interface (Beta)\n-------------------------------\n\nWe have also developed a graphical user interface (GUI) for **single-threaded**\nhybridization detection analyses with HyDe. Users can supply file names and other\noptions in the GUI window and hit ``Run`` or ``\u003cReturn\u003e`` to run analyses.\n\n.. image:: docs/img/gui.png\n   :align: center\n\nGetting Help\n------------\n\nIf you have questions about running HyDe, please feel free to use the\n**gitter chatroom** to get help:\n\n|Gitter|\n\nIf you have a problem while running HyDe and you think it may be a bug,\nplease consider filing an issue:\n\n|HyDe Issues|\n\nInstallation\n------------\n\nRequirements:\n~~~~~~~~~~~~~\n\n-  Python 3.9+\n-  Python Modules:\n\n   -  cython\n   -  numpy\n   -  multiprocess\n   -  progress (optional: needed for GUI)\n\n-  C++ compiler\n\n.. code:: bash\n\n    # To install dependencies -- add 'progress' if you're using the GUI\n    python3 -m pip install -r requirements.txt\n\n    # Clone HyDe repository from GitHub\n    git clone https://github.com/pblischak/HyDe.git\n    cd HyDe\n\n    # Now install phyde module\n    python3 -m pip install .\n\n    # Test the installation\n    make test\n\n    # Test multithreaded scripts\n    make test_threads\n\nThe ``phyde`` module is also hosted on the Python Package Index (PyPI), and can be installed directly using\n``pip``.\n\n.. code:: bash\n\n  # Install from PyPI with pip\n  pip install phyde\n\nDocumentation for analyzing data using HyDe can be found `here \u003chttp://hybridization-detection.readthedocs.io/analyze.html\u003e`_.\n\n.. |Documentation| image:: http://readthedocs.org/projects/hybridization-detection/badge/?version=latest\n   :target: http://hybridization-detection.readthedocs.io\n\n.. |PyPI Badge| image:: https://img.shields.io/pypi/v/phyde.svg\n   :target: https://pypi.python.org/pypi/phyde\n\n.. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg\n   :target: https://gitter.im/pblischak-HyDe/Lobby\n\n.. |HyDe Issues| image:: https://img.shields.io/badge/HyDe-Issues-blue.svg\n   :target: https://github.com/pblischak/HyDe/issues\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpblischak%2Fhyde","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpblischak%2Fhyde","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpblischak%2Fhyde/lists"}