{ "info": { "author": "Joshua Stevenson", "author_email": "joshua.stevenson@utas.edu.au", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3" ], "description": "\"SplitP\"\n\n[![](https://img.shields.io/pypi/v/SplitP.svg)](https://pypi.org/project/SplitP/) ![](https://github.com/js51/SplitP/workflows/build/badge.svg)\n[![Coverage Status](https://coveralls.io/repos/github/js51/SplitP/badge.svg?branch=main&service=github)](https://coveralls.io/github/js51/SplitP?branch=main)\n\nPython package which implements split- and rank-based tools for inferring phylogenies, such as _flattenings_ and _subflattenings_.\n\n### Installation\n\nThe latest version of SplitP can be installed via the command\n`pip install splitp`\n\n### Examples\n\nImport `splitp` and the associated helper functions\n```python\nimport splitp as sp\nfrom splitp import tree_helper_functions as hf\n```\nDefine trees and work with splits\n```python\nsplits = list(hf.all_splits(4)) # [01|23, 02|13, 03|12]\ntree = sp.NXTree('((0,1),(2,3));')\t\ntrue_splits = tree.true_splits() # 01|23\n```\nLet site patterns evolve under any submodel of the general markov model.\n```python\nJC_subs_matrix = tree.build_JC_matrix(branch_length:=0.05)\ntree.reassign_all_transition_matrices(JC_subs_matrix)\npattern_probs = tree.get_pattern_probabilities()\n```\n```css\n> 0 1\n 0 AAAA 0.185844\n 1 AAAC 0.003262\n .. ... ...\n 254 TTTG 0.003262\n 255 TTTT 0.185844\n```\nSimulate sequence alignments from pattern distributions\n```python\npattern_frequencies = tree.draw_from_multinomial(pattern_probs, 100)\n```\n```css\n> 0 1\n 0 AAAA 0.22\n 1 AAAC 0.01\n .. ... ...\n 2 CCGC 0.03\n 3 TTTT 0.14\n```\nReconstruct trees using split based methods including flattenings:\n```python\nF1 = tree.flattening('01|23', pattern_frequencies)\nF2 = tree.flattening('02|13', pattern_frequencies)\nprint(tree.split_score(F1) < tree.split_score(F2)) # True\n```\nOr subflattenings:\n```python\nSF = tree.signed_sum_subflattening('01|23', pattern_probs)\nprint(tree.split_score(SF)) # 0.0\n```\nFor more functionality please see the documentation at [splitp.joshuastevenson.me](http://splitp.joshuastevenson.me/splitp.html).\n\nPlease see `CONTRIBUTING.md` for information on contributing to this project.\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/js51/SplitP", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "splitp", "package_url": "https://pypi.org/project/splitp/", "platform": null, "project_url": "https://pypi.org/project/splitp/", "project_urls": { "Homepage": "https://github.com/js51/SplitP" }, "release_url": "https://pypi.org/project/splitp/0.1.8/", "requires_dist": null, "requires_python": ">=3.6", "summary": "Phylogenetic tools and methods involving splits and matrix rank", "version": "0.1.8", "yanked": false, "yanked_reason": null }, "last_serial": 13210252, "releases": { "0.0.0": [ { "comment_text": "", "digests": { "md5": "abc501a9961cea5c1214de313cc57682", "sha256": "02a3153e80ad418757a31db29f194be11b142ce6bab87f1edd0a576dca0ccaea" }, "downloads": -1, "filename": "splitp-0.0.0-py3-none-any.whl", "has_sig": false, "md5_digest": "abc501a9961cea5c1214de313cc57682", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 10636, "upload_time": "2020-03-05T03:13:32", "upload_time_iso_8601": "2020-03-05T03:13:32.715696Z", "url": "https://files.pythonhosted.org/packages/f9/66/fd909dbe32cafa6fb9b29c84fb3804d0f87e40de228e0460757fadde107a/splitp-0.0.0-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "4f87b6057e602929fea7e0ceaedc5e3c", "sha256": "688f87dac2de3dfed333f1ca02f4d6306ea99360acfbe8e05c4a506977dbc98a" }, "downloads": -1, "filename": "splitp-0.0.0.tar.gz", "has_sig": false, "md5_digest": "4f87b6057e602929fea7e0ceaedc5e3c", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 8779, "upload_time": "2020-03-05T03:13:35", "upload_time_iso_8601": "2020-03-05T03:13:35.308876Z", "url": "https://files.pythonhosted.org/packages/b8/92/c538a4cd939935c2ea446ccb8371e3b1068d000a3626cb7952a0f7f418cd/splitp-0.0.0.tar.gz", "yanked": false, "yanked_reason": null } ], "0.0.3": [ { "comment_text": "", "digests": { "md5": "b0c02c1a754a4a856bc64aa5e9ca273b", "sha256": "9a72d1aaf494c69ac97c7929a6c9a00fb9f74a234e4f96bca10d6dc19105372e" }, "downloads": -1, "filename": "SplitP-0.0.3-py3-none-any.whl", "has_sig": false, "md5_digest": "b0c02c1a754a4a856bc64aa5e9ca273b", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 9472, "upload_time": "2019-10-29T05:26:40", "upload_time_iso_8601": "2019-10-29T05:26:40.797482Z", "url": "https://files.pythonhosted.org/packages/b2/86/821e226f90bd06998d2b44fefe5f06895886909e91938c67afb788f78c35/SplitP-0.0.3-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "6fa682b1894cfc61f6497d178de3a603", "sha256": "9027188f627bebf82a4ae872ec2f85c7faaf542a8852973fdfe352948bef306e" }, "downloads": -1, "filename": "SplitP-0.0.3.tar.gz", "has_sig": false, "md5_digest": "6fa682b1894cfc61f6497d178de3a603", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 7738, "upload_time": "2019-10-29T05:26:42", "upload_time_iso_8601": "2019-10-29T05:26:42.039569Z", "url": "https://files.pythonhosted.org/packages/80/9a/449162d942bea78ee878ab9097c1b1aa619824e896bb0e8ba5a5b71189b0/SplitP-0.0.3.tar.gz", "yanked": false, "yanked_reason": null } ], "0.0.4": [ { "comment_text": "", "digests": { "md5": "ac441c02db91bf64ff11d0eb86f6d7b0", "sha256": "a4d4714d012a8f03a14d9543badf15abfac60046934f5057dd2779dd75049805" }, "downloads": -1, "filename": "SplitP-0.0.4-py3-none-any.whl", "has_sig": false, "md5_digest": "ac441c02db91bf64ff11d0eb86f6d7b0", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.5", "size": 9722, "upload_time": "2020-02-18T11:00:32", "upload_time_iso_8601": "2020-02-18T11:00:32.362386Z", "url": "https://files.pythonhosted.org/packages/67/2a/752fc5273986ce45f11b5eb4a035da0d86190a361e299d226e621dcc528e/SplitP-0.0.4-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "5df71f09f73cbc439fb887b551b98ba7", "sha256": "efecc797da99f7289372bacc25788a6b4045749686510e0ea6d60aaf6c3a9f8f" }, "downloads": -1, "filename": "SplitP-0.0.4.tar.gz", "has_sig": false, "md5_digest": "5df71f09f73cbc439fb887b551b98ba7", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.5", "size": 7964, "upload_time": "2020-02-18T11:00:33", "upload_time_iso_8601": "2020-02-18T11:00:33.311705Z", "url": "https://files.pythonhosted.org/packages/b3/f9/59b5c952404e1fd1879746a9b5c1e99132df99667c1b46a5ee979e83427e/SplitP-0.0.4.tar.gz", "yanked": false, "yanked_reason": null } ], "0.1.1": [ { "comment_text": "", "digests": { "md5": "09c1649d4184b77e617ac739b3711b27", "sha256": "29690fe1647e143cf612e65353d29120c402a80a9d29fe59e3c0947e8a5c274e" }, "downloads": -1, "filename": "splitp-0.1.1-py3-none-any.whl", "has_sig": false, "md5_digest": "09c1649d4184b77e617ac739b3711b27", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 10637, "upload_time": "2020-03-05T03:25:44", "upload_time_iso_8601": "2020-03-05T03:25:44.165797Z", "url": "https://files.pythonhosted.org/packages/e2/9e/13c24972e41b914230541d0b850cecc3f8b921226d7b30e46825b48257f6/splitp-0.1.1-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "0b72f742efa2e2ce4c0fa844ee642ac8", "sha256": "57477a3a6ebb6d0593bbdf0a68811cb399fa56f0524381af7ecbe328b4dadc25" }, "downloads": -1, "filename": "splitp-0.1.1.tar.gz", "has_sig": false, "md5_digest": "0b72f742efa2e2ce4c0fa844ee642ac8", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 8779, "upload_time": "2020-03-05T03:25:45", "upload_time_iso_8601": "2020-03-05T03:25:45.295628Z", "url": "https://files.pythonhosted.org/packages/85/10/16dc27b341e10b6f47ade743bd37a6d194d01711ddce89e608f779bd15cd/splitp-0.1.1.tar.gz", "yanked": false, "yanked_reason": null } ], "0.1.4": [ { "comment_text": "", "digests": { "md5": "845e30fd9fa650083725cef5ece7ca0a", "sha256": "413a86f740003ebed07cb103b82a2747baf3093aa74768d7cca181938da3bd53" }, "downloads": -1, "filename": "splitp-0.1.4-py3-none-any.whl", "has_sig": false, "md5_digest": "845e30fd9fa650083725cef5ece7ca0a", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 825497, "upload_time": "2021-02-22T11:12:30", "upload_time_iso_8601": "2021-02-22T11:12:30.433058Z", "url": "https://files.pythonhosted.org/packages/d1/23/ad7b7c3a07994c9a992327ccd7e813d9b282d2ad0ea9d6a75a069f091671/splitp-0.1.4-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "0f0161443417d8b262e3d92c0d511b26", "sha256": "6a8270f4443a1bf0a4c536ab36cf80772326a72d03d83639cc8b5acebbc963f3" }, "downloads": -1, "filename": "splitp-0.1.4.tar.gz", "has_sig": false, "md5_digest": "0f0161443417d8b262e3d92c0d511b26", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 821495, "upload_time": "2021-02-22T11:12:31", "upload_time_iso_8601": "2021-02-22T11:12:31.709570Z", "url": "https://files.pythonhosted.org/packages/8a/37/788cdaf56628ec29795e6bfdcb28233cab424d0e6fd078eac9d88c086a00/splitp-0.1.4.tar.gz", "yanked": false, "yanked_reason": null } ], "0.1.5": [ { "comment_text": "", "digests": { "md5": "8620cd18de5a4e586834cce353d0fd93", "sha256": "abf0c87ff057c60db2d93fba9c24e47eedab78dfce9e532171423315dcb4d01e" }, "downloads": -1, "filename": "splitp-0.1.5-py3-none-any.whl", "has_sig": false, "md5_digest": "8620cd18de5a4e586834cce353d0fd93", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 825988, "upload_time": "2021-02-24T00:47:04", "upload_time_iso_8601": "2021-02-24T00:47:04.979376Z", "url": "https://files.pythonhosted.org/packages/f8/a1/92baa624922cddcdba83df4fea25043d2ccb53344da04a5be0afdc4619c2/splitp-0.1.5-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "d886b778d9e24cbfa6363228bb015f52", "sha256": "1d17ca15d03afb5a57bc8d2af69f1cdfba40b3ee1ced4a78b7b5f3585d353316" }, "downloads": -1, "filename": "splitp-0.1.5.tar.gz", "has_sig": false, "md5_digest": "d886b778d9e24cbfa6363228bb015f52", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 822271, "upload_time": "2021-02-24T00:47:06", "upload_time_iso_8601": "2021-02-24T00:47:06.570992Z", "url": "https://files.pythonhosted.org/packages/7a/dd/ccd3bb7aaed0beb0def8ca52be1b0891654899f4a78e8faad7f644254fe1/splitp-0.1.5.tar.gz", "yanked": false, "yanked_reason": null } ], "0.1.7": [ { "comment_text": "", "digests": { "md5": "690f9cd19478091fdf9888fcb27bf131", "sha256": "80394efb3654729236a5d59556b2bf6ff9211999fbec086b9f31dab88a54aa78" }, "downloads": -1, "filename": "splitp-0.1.7-py3-none-any.whl", "has_sig": false, "md5_digest": "690f9cd19478091fdf9888fcb27bf131", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 829420, "upload_time": "2021-07-01T05:18:25", "upload_time_iso_8601": "2021-07-01T05:18:25.856806Z", "url": "https://files.pythonhosted.org/packages/9d/e4/1bac023d512dae4360398d0b7b7336a77610bdc9d0bc399030d2299be4e5/splitp-0.1.7-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "2c24c63849672382a17dfe8326ce30eb", "sha256": "d0bc515e6d7a5bce691155c81140a43673c80c777124da0b9e837adea664560d" }, "downloads": -1, "filename": "splitp-0.1.7.tar.gz", "has_sig": false, "md5_digest": "2c24c63849672382a17dfe8326ce30eb", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 827146, "upload_time": "2021-07-01T05:18:27", "upload_time_iso_8601": "2021-07-01T05:18:27.266155Z", "url": "https://files.pythonhosted.org/packages/ff/af/1be37dab60cb7dc4cadbe11a2587e6d93f211bbd27fcd13d7e9fd8094093/splitp-0.1.7.tar.gz", "yanked": false, "yanked_reason": null } ], "0.1.8": [ { "comment_text": "", "digests": { "md5": "12404acb26445281f6c06b7ea7d58068", "sha256": "fedaa932b6758af4979bbbb6b648f38eebcef62739f0c10cf6a334197a9f12a2" }, "downloads": -1, "filename": "splitp-0.1.8-py3-none-any.whl", "has_sig": false, "md5_digest": "12404acb26445281f6c06b7ea7d58068", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 830231, "upload_time": "2022-03-17T23:31:45", "upload_time_iso_8601": "2022-03-17T23:31:45.109289Z", "url": "https://files.pythonhosted.org/packages/31/42/213e041e19db8d3595fe65396c9535afcc1cf87ca4807df61dfc228f0c6a/splitp-0.1.8-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "6e84be8b1ec4349d0486a045305bd2f5", "sha256": "a5c72dc8cdee9871307688573c6dbe7a346c9c4c84371badbe3db6bff223c55b" }, "downloads": -1, "filename": "splitp-0.1.8.tar.gz", "has_sig": false, "md5_digest": "6e84be8b1ec4349d0486a045305bd2f5", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 827365, "upload_time": "2022-03-17T23:31:46", "upload_time_iso_8601": "2022-03-17T23:31:46.677821Z", "url": "https://files.pythonhosted.org/packages/ab/8e/cacb86b1b58aab838888d03f765169bf87d5b1826a946db8dc5548171b0c/splitp-0.1.8.tar.gz", "yanked": false, "yanked_reason": null } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "12404acb26445281f6c06b7ea7d58068", "sha256": "fedaa932b6758af4979bbbb6b648f38eebcef62739f0c10cf6a334197a9f12a2" }, "downloads": -1, "filename": "splitp-0.1.8-py3-none-any.whl", "has_sig": false, "md5_digest": "12404acb26445281f6c06b7ea7d58068", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 830231, "upload_time": "2022-03-17T23:31:45", "upload_time_iso_8601": "2022-03-17T23:31:45.109289Z", "url": "https://files.pythonhosted.org/packages/31/42/213e041e19db8d3595fe65396c9535afcc1cf87ca4807df61dfc228f0c6a/splitp-0.1.8-py3-none-any.whl", "yanked": false, "yanked_reason": null }, { "comment_text": "", "digests": { "md5": "6e84be8b1ec4349d0486a045305bd2f5", "sha256": "a5c72dc8cdee9871307688573c6dbe7a346c9c4c84371badbe3db6bff223c55b" }, "downloads": -1, "filename": "splitp-0.1.8.tar.gz", "has_sig": false, "md5_digest": "6e84be8b1ec4349d0486a045305bd2f5", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 827365, "upload_time": "2022-03-17T23:31:46", "upload_time_iso_8601": "2022-03-17T23:31:46.677821Z", "url": "https://files.pythonhosted.org/packages/ab/8e/cacb86b1b58aab838888d03f765169bf87d5b1826a946db8dc5548171b0c/splitp-0.1.8.tar.gz", "yanked": false, "yanked_reason": null } ], "vulnerabilities": [] }