{ "info": { "author": "the Bloom lab (see https://github.com/jbloomlab/phydms/contributors)", "author_email": "jbloom@fredhutch.org", "bugtrack_url": null, "classifiers": [], "description": "========================\n``phydms``\n========================\n.. image:: https://travis-ci.org/jbloomlab/phydms.svg?branch=master\n :target: https://travis-ci.org/jbloomlab/phydms\n\n``phydms`` enables **phy**\\logenetic analyses using **d**\\eep **m**\\utational **s**\\canning data to inform the substitution models. It implements **Exp**\\erimentally informed **c**\\odon **m**\\odels (*ExpCM*) for phylogenetic inference and the detection of biologically interesting selection.\n\n``phydms`` is written by the `Bloom lab`_ (see https://github.com/jbloomlab/phydms/contributors for a full list of contributors).\n\nSee the `phydms documentation`_ for information about using ``phydms`` and details about the recommended installation process.\n\nThe `phydms source code`_ is freely available under a `GPLv3`_ license.\n\nIf you use ``phydms``, please `cite it appropriately`_.\n\n\n.. _`Jesse Bloom`: http://research.fhcrc.org/bloom/en.html\n.. _`phydms documentation`: http://jbloomlab.github.io/phydms/\n.. _`phydms source code`: https://github.com/jbloomlab/phydms\n.. _`GPLv3`: http://www.gnu.org/copyleft/gpl.html\n.. _`Bloom lab`: http://labs.fhcrc.org/bloom\n.. _`cite it appropriately`: http://jbloomlab.github.io/phydms/acknowledgments.html", "description_content_type": "", "docs_url": null, "download_url": "https://github.com/jbloomlab/phydms/tarball/2.3.3", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://jbloomlab.github.io/phydms", "keywords": "", "license": "GPLv3", "maintainer": "", "maintainer_email": "", "name": "phydms", "package_url": "https://pypi.org/project/phydms/", "platform": "", "project_url": "https://pypi.org/project/phydms/", "project_urls": { "Download": "https://github.com/jbloomlab/phydms/tarball/2.3.3", "Homepage": "http://jbloomlab.github.io/phydms" }, "release_url": "https://pypi.org/project/phydms/2.3.3/", "requires_dist": null, "requires_python": "", "summary": "Phylogenetic analyses informed by deep mutational scanning data.", "version": "2.3.3" }, "last_serial": 5574751, "releases": { "1.0.0": [ { "comment_text": "", "digests": { "md5": "ebd58b340a9322de75f6f289e4ea9e9a", "sha256": "28f8fe31062699196a4dbacf76d3ff511730d04cccd0fe7c337b6b4c14dfa023" }, "downloads": -1, "filename": "phydms-1.0.0.tar.gz", "has_sig": false, "md5_digest": "ebd58b340a9322de75f6f289e4ea9e9a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2499499, "upload_time": "2016-01-05T14:49:18", "url": "https://files.pythonhosted.org/packages/11/8b/924f010cb273c3d58b5ebca589d32044b7d38f2355a3e4018596a926b5a3/phydms-1.0.0.tar.gz" } ], "1.0.1": [ { "comment_text": "", "digests": { "md5": "4f5a57770ec2ab1b49804e0496506f13", "sha256": "4a5a2ccb4f4d64db9a8ff6211653a2c27e6594995dacafda80a2f09464dc3924" }, "downloads": -1, "filename": "phydms-1.0.1.tar.gz", "has_sig": false, "md5_digest": "4f5a57770ec2ab1b49804e0496506f13", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2593987, "upload_time": "2016-01-05T15:07:22", "url": "https://files.pythonhosted.org/packages/6f/19/f8d04c628f5d06cb911a58cfa6b53988298500bdaeea689695a1d1801595/phydms-1.0.1.tar.gz" } ], "1.0.2": [ { "comment_text": "", "digests": { "md5": "e0bfc798506df8ea8d14406545599001", "sha256": "0a9f45574b40c4889273d21e15d1f409a81b53e7b92f46233dde09f820eb36d9" }, "downloads": -1, "filename": "phydms-1.0.2.tar.gz", "has_sig": false, "md5_digest": "e0bfc798506df8ea8d14406545599001", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2594113, "upload_time": "2016-01-15T19:19:58", "url": "https://files.pythonhosted.org/packages/7a/9e/d72b19e0423c6347f7d2a3ee341e6c7d95762391a5f4727c71c55cd36315/phydms-1.0.2.tar.gz" } ], "1.1.0": [ { "comment_text": "", "digests": { "md5": "884915803952278f510b61e373938452", "sha256": "ee376ab454e30059e87c6045a2b355fabd4870be4007082a55c82bae21e5fe7b" }, "downloads": -1, "filename": "phydms-1.1.0.tar.gz", "has_sig": false, "md5_digest": "884915803952278f510b61e373938452", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2645421, "upload_time": "2016-02-20T06:54:22", "url": "https://files.pythonhosted.org/packages/97/04/aff84721a0b84aaf193e5cd4e03afc481959566ed1d89903d6157f682bbf/phydms-1.1.0.tar.gz" } ], "1.2.0": [ { "comment_text": "", "digests": { "md5": "99fd233fc02299d03f4964bf8a6498c3", "sha256": "594107afd6b2cc29701093c4b3a88da9901e9aa316222f61d9e325fa695d44ce" }, "downloads": -1, "filename": "phydms-1.2.0.tar.gz", "has_sig": false, "md5_digest": "99fd233fc02299d03f4964bf8a6498c3", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2813419, "upload_time": "2016-03-14T05:03:58", "url": "https://files.pythonhosted.org/packages/b8/a4/9a766d44bdddb39d4b27970590671065ccaad8bf6f2c103d4cba4860e6e6/phydms-1.2.0.tar.gz" } ], "1.2.1": [ { "comment_text": "", "digests": { "md5": "4b24009652233a1712b404b326b4dcde", "sha256": "c3487b938aa93d21b5b478e6e9124efb375b730c960848cf3f0d7725edfaa352" }, "downloads": -1, "filename": "phydms-1.2.1.tar.gz", "has_sig": false, "md5_digest": "4b24009652233a1712b404b326b4dcde", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2807645, "upload_time": "2016-03-31T02:20:21", "url": "https://files.pythonhosted.org/packages/89/8d/0fda131f5a9c10f1b0c5f9a07d45aa5a488c6504b2991acf6bd43cee0087/phydms-1.2.1.tar.gz" } ], "1.2.2": [ { "comment_text": "", "digests": { "md5": "20de2c7d7c11b5d10942951af596baff", "sha256": "56117e112039a4cb778b76572d46780ba96cb5b9eaec05c4aad5bda8ec4f4883" }, "downloads": -1, "filename": "phydms-1.2.2.tar.gz", "has_sig": false, "md5_digest": "20de2c7d7c11b5d10942951af596baff", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2814209, "upload_time": "2016-04-05T03:09:39", "url": "https://files.pythonhosted.org/packages/cf/1d/bcc6f877c3129cd15943bcdaaac04707799d698827a2a171c30c94854d26/phydms-1.2.2.tar.gz" } ], "1.2.3": [ { "comment_text": "", "digests": { "md5": "115b9d97413bef59cbe000fa279c8f5c", "sha256": "a4d8bba85902503840486a2c4a54fd15231f4367fde00a96e32f4739c17908a5" }, "downloads": -1, "filename": "phydms-1.2.3.tar.gz", "has_sig": false, "md5_digest": "115b9d97413bef59cbe000fa279c8f5c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2814945, "upload_time": "2016-07-15T19:35:00", "url": "https://files.pythonhosted.org/packages/af/f0/7be30b868a70e2d56f14e956dc89fa29fb6423ffc40cc5ea2a4b7e5a1da3/phydms-1.2.3.tar.gz" } ], "1.2.4": [ { "comment_text": "", "digests": { "md5": "920bbad47154dcaf36020baeaf3996c7", "sha256": "15de1268b9ccff63b8d5dce1af42fce0b74d785ef55c740f9f9884cfcb00568e" }, "downloads": -1, "filename": "phydms-1.2.4.tar.gz", "has_sig": false, "md5_digest": "920bbad47154dcaf36020baeaf3996c7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2818429, "upload_time": "2016-07-31T16:49:42", "url": "https://files.pythonhosted.org/packages/bc/6a/8359a5c0574156f52584ca5af73006ca00ad22ada8e0a5043045ad2351a8/phydms-1.2.4.tar.gz" } ], "1.2.5": [ { "comment_text": "", "digests": { "md5": "def677ea9ef054888a82ac9b0c7ade8c", "sha256": "490d6d14bf61a156815f0301e010d972d4c6661d8dfc0ba88baae1f7a752cc49" }, "downloads": -1, "filename": "phydms-1.2.5.tar.gz", "has_sig": false, "md5_digest": "def677ea9ef054888a82ac9b0c7ade8c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2819547, "upload_time": "2016-08-13T18:48:20", "url": "https://files.pythonhosted.org/packages/95/94/83ad1639e1b4f5443f4f87a02808f1baa343443b3bc6bd56d1dfd62101bd/phydms-1.2.5.tar.gz" } ], "1.3.0": [ { "comment_text": "", "digests": { "md5": "9c3d76e4d2d6df883cc09137e3218ef6", "sha256": "06ed1fad6a3b0c1ad9be57ddb785b0ed570fda7fd22e669de49d6a1a1b28eb00" }, "downloads": -1, "filename": "phydms-1.3.0.tar.gz", "has_sig": false, "md5_digest": "9c3d76e4d2d6df883cc09137e3218ef6", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 2615186, "upload_time": "2016-10-05T19:37:54", "url": "https://files.pythonhosted.org/packages/95/4a/69ec601ce4654d6c91c614e12122a3e1ba1b7a02275e38c0aaa15246cb64/phydms-1.3.0.tar.gz" } ], "2.0.0": [ { "comment_text": "", "digests": { "md5": "541cdc7e12786da012c0c23fc5a295aa", "sha256": "1db0c03642c75eede6cdbf64a102c45c3a5ab04999e2e75d049a3f97e2a7b0fa" }, "downloads": -1, "filename": "phydms-2.0.0.tar.gz", "has_sig": false, "md5_digest": "541cdc7e12786da012c0c23fc5a295aa", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 586924, "upload_time": "2017-03-13T20:33:07", "url": "https://files.pythonhosted.org/packages/c9/26/1663b6f3005d5e2c280ebaa2bca84251710ea7eb81a63ce2ef6d753577ae/phydms-2.0.0.tar.gz" } ], "2.0.1": [ { "comment_text": "", "digests": { "md5": "98888adecfc117f03813553a11424eca", "sha256": "fea9fef5140294461020f830dbf1902d06291fc9d7278b4b865fc8e4c3942dba" }, "downloads": -1, "filename": "phydms-2.0.1.tar.gz", "has_sig": false, "md5_digest": "98888adecfc117f03813553a11424eca", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 583967, "upload_time": "2017-03-29T18:23:23", "url": "https://files.pythonhosted.org/packages/3d/a6/7f55eca9d765e342a1726e6ec8e2ad1595b3d1d80eeb83bba8d6c7774db9/phydms-2.0.1.tar.gz" } ], "2.0.2": [ { "comment_text": "", "digests": { "md5": "16ea9a860b78c3e85bf8eba1d1933409", "sha256": "d47a40f8c600c2936fbf2e78727fbf4e3e528b9e64b978930cc597159d1d9291" }, "downloads": -1, "filename": "phydms-2.0.2.tar.gz", "has_sig": false, "md5_digest": "16ea9a860b78c3e85bf8eba1d1933409", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 585504, "upload_time": "2017-04-15T06:03:51", "url": "https://files.pythonhosted.org/packages/21/ba/99e6c7d184abf29f1948f423c8d4f3131b547570e066fec231719fbb1891/phydms-2.0.2.tar.gz" } ], "2.0.3": [ { "comment_text": "", "digests": { "md5": "c88daa4cc50405abfd9aa735a40e2272", "sha256": "3c7e37c6c8ee6c8ecd0d619718c7c809e61c83b23465185e1d7e860c646c74e5" }, "downloads": -1, "filename": "phydms-2.0.3.tar.gz", "has_sig": false, "md5_digest": "c88daa4cc50405abfd9aa735a40e2272", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 585786, "upload_time": "2017-04-17T20:44:13", "url": "https://files.pythonhosted.org/packages/a8/8e/91ee2e972a9837b0eb948696887c690c9dba13fc51b7cfddd755a69a9ebe/phydms-2.0.3.tar.gz" } ], "2.0.4": [ { "comment_text": "", "digests": { "md5": "875b74edad622333f4a0ee1c85101878", "sha256": "42051e72175f6093b44323a97bb3435d7fdcd407951cae237c22b12910c8b664" }, "downloads": -1, "filename": "phydms-2.0.4.tar.gz", "has_sig": false, "md5_digest": "875b74edad622333f4a0ee1c85101878", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 586973, "upload_time": "2017-05-12T21:47:38", "url": "https://files.pythonhosted.org/packages/39/9a/79c9350297cd356d5b85f21ae368af4c2f6feb579e464a26b4f3033044e1/phydms-2.0.4.tar.gz" } ], "2.0.5": [ { "comment_text": "", "digests": { "md5": "b7ae33265e1c2da95688e4f066ab03a7", "sha256": "8c6c1d69ceef92ba113b49aed6bc62b9fd738cc1f1aa31772ee2d6456c8dafbf" }, "downloads": -1, "filename": "phydms-2.0.5.tar.gz", "has_sig": false, "md5_digest": "b7ae33265e1c2da95688e4f066ab03a7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 587266, "upload_time": "2017-05-17T17:32:51", "url": "https://files.pythonhosted.org/packages/5f/20/e6b2886824048f55f96c74b582635240fe379901fcc2ae9cc16d805e1e67/phydms-2.0.5.tar.gz" } ], "2.1.0": [ { "comment_text": "", "digests": { "md5": "b63753e8bc49c2647c830d752b6e1018", "sha256": "79d456f886cfaf626ef99df9aabae72f5d113cffa6a23bc17aa1f011dfba283c" }, "downloads": -1, "filename": "phydms-2.1.0.tar.gz", "has_sig": false, "md5_digest": "b63753e8bc49c2647c830d752b6e1018", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 591236, "upload_time": "2017-08-31T21:11:17", "url": "https://files.pythonhosted.org/packages/99/34/b560ee996e5e8b6b264c817aed8677ce28ac81e4287c6c70c8c95cf21c93/phydms-2.1.0.tar.gz" } ], "2.1.1": [ { "comment_text": "", "digests": { "md5": "30a35a9e6969dfc019b90fda071a6c59", "sha256": "7cd0f452a963fde64cc808cee8d198fdef4a1d81b5379c5aad2bf47ca0c1c852" }, "downloads": -1, "filename": "phydms-2.1.1.tar.gz", "has_sig": false, "md5_digest": "30a35a9e6969dfc019b90fda071a6c59", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 590029, "upload_time": "2017-09-01T00:05:10", "url": "https://files.pythonhosted.org/packages/c5/a3/041d15a1abbf422ac6f1c91eb23ba0db1e50777dba5a64e6df7fa2140871/phydms-2.1.1.tar.gz" } ], "2.1.2": [ { "comment_text": "", "digests": { "md5": "b348f0ae43eba709886d8cf6bda1e596", "sha256": "7e7c970a7a73e730d57611edf2061f89d2e4b7f89c7f70ec2dbd912d5df759ba" }, "downloads": -1, "filename": "phydms-2.1.2.tar.gz", "has_sig": false, "md5_digest": "b348f0ae43eba709886d8cf6bda1e596", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 591980, "upload_time": "2017-09-19T15:32:05", "url": "https://files.pythonhosted.org/packages/64/71/bdc4e1435808360148cfb1e94a23cb90699d8d8b2b90591d0b2776ae12de/phydms-2.1.2.tar.gz" } ], "2.1.3": [ { "comment_text": "", "digests": { "md5": "cf3f9a5444cb8727c911583abd256dfd", "sha256": "36ca87804ba5e580aa0d16ab1f55b15eea3af76afbe0c4938887e001b6424ece" }, "downloads": -1, "filename": "phydms-2.1.3.tar.gz", "has_sig": false, "md5_digest": "cf3f9a5444cb8727c911583abd256dfd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 592575, "upload_time": "2017-10-03T15:28:52", "url": "https://files.pythonhosted.org/packages/30/6b/f6a25dc2940fd2fe23489136fa1c5e6c013114f9f35423be6a0242b6b161/phydms-2.1.3.tar.gz" } ], "2.1.4": [ { "comment_text": "", "digests": { "md5": "197eac11d16a0e4c4e799eadaef00552", "sha256": "048fec8aae41f4cf18ccd9e8f0c0980f654290dd9ce01b37e4f1f950ea54c78b" }, "downloads": -1, "filename": "phydms-2.1.4.tar.gz", "has_sig": false, "md5_digest": "197eac11d16a0e4c4e799eadaef00552", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 593534, "upload_time": "2017-10-25T15:37:58", "url": "https://files.pythonhosted.org/packages/4c/5c/d575b084b454df2d4596c258d61de9ce637f19e028eb3d64b31ffb120e3d/phydms-2.1.4.tar.gz" } ], "2.2.0": [ { "comment_text": "", "digests": { "md5": "611fb952f2bf29d9080e5aad9e461f4f", "sha256": "9094114c44bb944e816e5baaa71e11d106112f993ce31e6531e36f4d358ea1cb" }, "downloads": -1, "filename": "phydms-2.2.0.tar.gz", "has_sig": false, "md5_digest": "611fb952f2bf29d9080e5aad9e461f4f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 595011, "upload_time": "2017-10-29T22:10:52", "url": "https://files.pythonhosted.org/packages/f0/f7/3881d836491bb3c0b174925c731ea595ddab5ed78cfe09f1e5221477cb86/phydms-2.2.0.tar.gz" } ], "2.2.1": [ { "comment_text": "", "digests": { "md5": "76ac48cd47aa1be0e928b617e9c8e7f1", "sha256": "702749858c1811b824ad0cd026c8cbfbd80961511cdfc06d6605746edf269eb3" }, "downloads": -1, "filename": "phydms-2.2.1.tar.gz", "has_sig": false, "md5_digest": "76ac48cd47aa1be0e928b617e9c8e7f1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 594339, "upload_time": "2018-01-25T22:07:58", "url": "https://files.pythonhosted.org/packages/4f/b5/e90d6505b94c2a0a383d9ef281247366ba7e6d40770107df276f511b1e8c/phydms-2.2.1.tar.gz" } ], "2.2.2": [ { "comment_text": "", "digests": { "md5": "55327455f8c8299897a39883dbb63062", "sha256": "c85ad79c851bbcbd9c6c8e5515e92138c539d5bab7861f0ae3ac82a036c5ff0c" }, "downloads": -1, "filename": "phydms-2.2.2.tar.gz", "has_sig": false, "md5_digest": "55327455f8c8299897a39883dbb63062", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 594431, "upload_time": "2018-03-12T02:22:23", "url": "https://files.pythonhosted.org/packages/7b/ec/541e7deb49c50b1d154c54e7446c27aa132f279ceb8dd7cef39aa5cfd5d8/phydms-2.2.2.tar.gz" } ], "2.3.0": [ { "comment_text": "", "digests": { "md5": "b01be7d18c3186c8ac614bd87989949a", "sha256": "9031830847e875f9bee68f233740bf7e634131737cc7f7d490da84760a149c73" }, "downloads": -1, "filename": "phydms-2.3.0.tar.gz", "has_sig": false, "md5_digest": "b01be7d18c3186c8ac614bd87989949a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 227200, "upload_time": "2018-06-20T02:48:31", "url": "https://files.pythonhosted.org/packages/4c/ff/cf382034d5ceef9c4a6e60fbe8db814239039cf3282dbf461c2b9120ea4d/phydms-2.3.0.tar.gz" } ], "2.3.1": [ { "comment_text": "", "digests": { "md5": "0aad00ef5a2ad295faebe32acbb05823", "sha256": "163681770b1e97e9c8fdbbebebd3b3296fd046d5ee48058ea3929f6a4a7ea1bb" }, "downloads": -1, "filename": "phydms-2.3.1.tar.gz", "has_sig": false, "md5_digest": "0aad00ef5a2ad295faebe32acbb05823", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 230497, "upload_time": "2018-07-23T17:42:52", "url": "https://files.pythonhosted.org/packages/2a/fc/8487f272f7436859fd869c9e01ee742c0f41d369593baf9fb063625b08cc/phydms-2.3.1.tar.gz" } ], "2.3.2": [ { "comment_text": "", "digests": { "md5": "8151b3ed7de3c5b264c24a7f03000896", "sha256": "7ec6cdf59600907f967ff9e6a811425a1f1e955bd1f14c910108660e52947e75" }, "downloads": -1, "filename": "phydms-2.3.2.tar.gz", "has_sig": false, "md5_digest": "8151b3ed7de3c5b264c24a7f03000896", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 231886, "upload_time": "2019-06-09T22:04:16", "url": "https://files.pythonhosted.org/packages/42/e3/9ce35b49c05d49740b734134e122735c46382c494a6edffa594389afe0bd/phydms-2.3.2.tar.gz" } ], "2.3.3": [ { "comment_text": "", "digests": { "md5": "ec22b60c958fbdaf1022d8d15de0c331", "sha256": "d92864e016ec049eea6b1e5b49d7025c613a25ac58a4d719f383f3f305b92749" }, "downloads": -1, "filename": "phydms-2.3.3.tar.gz", "has_sig": false, "md5_digest": "ec22b60c958fbdaf1022d8d15de0c331", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 232104, "upload_time": "2019-07-23T22:34:29", "url": "https://files.pythonhosted.org/packages/82/fd/5aefb8ec8a1523c6cf5af53fb3d8e332e56cd97f7b02b85ceca8ecf90598/phydms-2.3.3.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "ec22b60c958fbdaf1022d8d15de0c331", "sha256": "d92864e016ec049eea6b1e5b49d7025c613a25ac58a4d719f383f3f305b92749" }, "downloads": -1, "filename": "phydms-2.3.3.tar.gz", "has_sig": false, "md5_digest": "ec22b60c958fbdaf1022d8d15de0c331", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 232104, "upload_time": "2019-07-23T22:34:29", "url": "https://files.pythonhosted.org/packages/82/fd/5aefb8ec8a1523c6cf5af53fb3d8e332e56cd97f7b02b85ceca8ecf90598/phydms-2.3.3.tar.gz" } ] }