{
    "info": {
        "author": "Jonathan Chang",
        "author_email": "jonathan.chang@ucla.edu",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
        ],
        "description": "# TACT - Taxonomy addition for complete trees\n\n[![PyPI](https://img.shields.io/pypi/v/tact.svg)](https://pypi.org/project/tact/)\n\nAdds tips to a backbone phylogeny using taxonomy simulated with birth-death models\n\n# Installation\n\nTACT requires Python 3. When possible, we recommend using the PyPy 3 implementation as it can significantly speed up TACT analyses, particularly on large datasets. In addition, TACT depends on the click, DendroPy, NumPy, and SciPy packages.\n\n## Homebrew\n\nUsing Homebrew is the recommended way to install TACT. [Install Homebrew on macOS](https://brew.sh) or [Install Homebrew on Linux or Windows 10](https://docs.brew.sh/Homebrew-on-Linux). Once Homebrew has been installed, run\n\n    brew install jonchang/biology/tact\n\n## pipx\n\nIf you are unable or unwilling to use Homebrew, the next recommended way to install TACT is via `pipx`. [Install `pipx`](https://github.com/pipxproject/pipx#install-pipx), then run:\n\n    pipx install tact\n\n## Other\n\nOther ways of installing TACT, including unpacking the tarball somewhere or directly using `pip`, are neither supported nor recommended.\n\n# Example\n\nFiles used are in the [examples](https://github.com/jonchang/tact/tree/master/examples) folder.\n\n```console\ncurl -LO https://raw.githubusercontent.com/jonchang/tact/master/examples/Carangaria.csv\ncurl -LO https://raw.githubusercontent.com/jonchang/tact/master/examples/Carangaria.tre\n```\n\nBuild a taxonomic tree using the provided CSV file. Run `tact_build_taxonomic_tree --help` to see the required format for this file.\n\n```console\n$ tact_build_taxonomic_tree Carangaria.csv --output Carangaria.taxonomy.tre\nOutput written to: Carangaria.taxonomy.tre\n```\n\n`Carangaria.taxonomy.tre` now contains a Newick phylogeny with many polytomies and named nodes indicating relevant taxonomic ranks. Now run the TACT stochastic polytomy resolver algorithm in conjunction with the backbone phylogeny `Caragaria.tre`.\n\n```console\n$ tact_add_taxa --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre --output Carangaria.tacted --verbose --verbose\nRates  [####################################]  226/226\nTACT  [####################################]  642/642  Carangaria\n```\n\nThere will be several files created with the prefix `Carangaria.tacted`. These include `newick.tre` and `nexus.tre` (your primary output in the form of Newick and NEXUS format phylogenies), `rates.csv` (estimated diversification rates on the backbone phylogeny), and `log.txt` (extremely verbose output on what TACT is doing and why).\n\nYou should check the TACT results now for any issues:\n\n```console\n$ tact_check_results Carangaria.tacted.newick.tre --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre > checkresults.csv\n```\n\nOpen up `checkresults.csv` in your favorite spreadsheet viewer and check the `warnings` column for any issues.\n\n# Citation\n\nThe manuscript for TACT is currently in review.\n\nTACT owes its existence to much foundational work in the area of stochastic polytomy resolution, namely PASTIS and CorSiM.\n\n* Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. O. (2013). PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011\u20131017. doi:[10.1111/2041-210x.12117](https://doi.org/10.1111/2041-210X.12117)\n\n* Cusimano, N., Stadler, T., & Renner, S. S. (2012). A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies. Systematic Biology, 61(5), 785\u2013792. doi:[10.1093/sysbio/sys031](https://doi.org/10.1093/sysbio/sys031)\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/jonchang/tact",
        "keywords": "",
        "license": "MIT",
        "maintainer": "Jonathan Chang",
        "maintainer_email": "jonathan.chang@ucla.edu",
        "name": "tact",
        "package_url": "https://pypi.org/project/tact/",
        "platform": "",
        "project_url": "https://pypi.org/project/tact/",
        "project_urls": {
            "Homepage": "https://github.com/jonchang/tact",
            "Repository": "https://github.com/jonchang/tact"
        },
        "release_url": "https://pypi.org/project/tact/0.2.0/",
        "requires_dist": [
            "scipy (>=1.3,<2.0)",
            "numpy (>=1.17,<2.0)",
            "click (>=7.0,<8.0)",
            "DendroPy (>=4.4,<5.0)"
        ],
        "requires_python": ">=3.6,<4.0",
        "summary": "Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models",
        "version": "0.2.0"
    },
    "last_serial": 5882844,
    "releases": {
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "78953b59df33af4acd0d6030e3cfcd67",
                    "sha256": "5e7b5ee2efacad0c6f85f39459c715b21c8468fe5bf2d29cead44d634244ccd4"
                },
                "downloads": -1,
                "filename": "tact-0.1.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "78953b59df33af4acd0d6030e3cfcd67",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 20314,
                "upload_time": "2019-07-24T09:04:10",
                "url": "https://files.pythonhosted.org/packages/44/bf/f9862c0507e5450d3cc835f5c365c5248a35c5aecaa14d6ff89dfeca119c/tact-0.1.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "38980316638cb4a1c9794ceee8f6f9bf",
                    "sha256": "02438ed805cbe430394454e7e8c01d8736833f688ceb2cb69f7a43ad1903c899"
                },
                "downloads": -1,
                "filename": "tact-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "38980316638cb4a1c9794ceee8f6f9bf",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 19537,
                "upload_time": "2019-07-24T09:04:12",
                "url": "https://files.pythonhosted.org/packages/72/3c/69309df15808028818f866df37f5ff792c15e9031652963c1dfdaf7158ad/tact-0.1.2.tar.gz"
            }
        ],
        "0.1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "d0c58a9ea7dd473ca2025a8af475f81c",
                    "sha256": "b3597c94941a51c4dc606f93aabb51e9be2a180f8edb8e5ef6a469905b390d0b"
                },
                "downloads": -1,
                "filename": "tact-0.1.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "d0c58a9ea7dd473ca2025a8af475f81c",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 18723,
                "upload_time": "2019-09-24T05:23:18",
                "url": "https://files.pythonhosted.org/packages/c5/69/afea70bd6f38f9a3b66e004af2194cd09a1db0d6a48ea7c7830ae3c89848/tact-0.1.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "4c6a0fdbb170a53321fa7d85c5f8f97e",
                    "sha256": "4e68d776e2730c1ad67aa0c668552f9f6240cde93e2f3f57accc0c7bf1a85a39"
                },
                "downloads": -1,
                "filename": "tact-0.1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "4c6a0fdbb170a53321fa7d85c5f8f97e",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 18124,
                "upload_time": "2019-09-24T05:23:19",
                "url": "https://files.pythonhosted.org/packages/b2/52/6242fb418c4dc41bead109f9f0efc9e0f60341d46840a5fa07b5093cb3e7/tact-0.1.4.tar.gz"
            }
        ],
        "0.2.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0b132f9da156f7c0c204dd305a45acee",
                    "sha256": "f70fe02f5068c51eb9a57bb9a24a29971723dc5606010678fb768cff96abf920"
                },
                "downloads": -1,
                "filename": "tact-0.2.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "0b132f9da156f7c0c204dd305a45acee",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 18836,
                "upload_time": "2019-09-25T03:26:24",
                "url": "https://files.pythonhosted.org/packages/b5/6d/0eacb7333565d5c846cdc67fad861aa2fbdf13dc1a3af61fde5b62027216/tact-0.2.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "2dfd2448df3590a1f37c2816c63d1196",
                    "sha256": "670b3f1a8494968b94d308a7ea633848c5ebe912109e0ffe02ce6c25e5d03746"
                },
                "downloads": -1,
                "filename": "tact-0.2.0.tar.gz",
                "has_sig": false,
                "md5_digest": "2dfd2448df3590a1f37c2816c63d1196",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 18239,
                "upload_time": "2019-09-25T03:26:26",
                "url": "https://files.pythonhosted.org/packages/f9/47/2efb4bb644ca4f5b0efd6be25ef5ba3dc4eba2d9832ca5ee0578fd3dd87c/tact-0.2.0.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "0b132f9da156f7c0c204dd305a45acee",
                "sha256": "f70fe02f5068c51eb9a57bb9a24a29971723dc5606010678fb768cff96abf920"
            },
            "downloads": -1,
            "filename": "tact-0.2.0-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "0b132f9da156f7c0c204dd305a45acee",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.6,<4.0",
            "size": 18836,
            "upload_time": "2019-09-25T03:26:24",
            "url": "https://files.pythonhosted.org/packages/b5/6d/0eacb7333565d5c846cdc67fad861aa2fbdf13dc1a3af61fde5b62027216/tact-0.2.0-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "2dfd2448df3590a1f37c2816c63d1196",
                "sha256": "670b3f1a8494968b94d308a7ea633848c5ebe912109e0ffe02ce6c25e5d03746"
            },
            "downloads": -1,
            "filename": "tact-0.2.0.tar.gz",
            "has_sig": false,
            "md5_digest": "2dfd2448df3590a1f37c2816c63d1196",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6,<4.0",
            "size": 18239,
            "upload_time": "2019-09-25T03:26:26",
            "url": "https://files.pythonhosted.org/packages/f9/47/2efb4bb644ca4f5b0efd6be25ef5ba3dc4eba2d9832ca5ee0578fd3dd87c/tact-0.2.0.tar.gz"
        }
    ]
}