{
    "info": {
        "author": "Nextstrain developers",
        "author_email": "trevor@bedford.io, richard.neher@unibas.ch",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: GNU Affero General Public License v3",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# Introduction\n\nNextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.\nWe provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.\nOur goal is to aid epidemiological understanding and improve outbreak response.\n\nResulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).\nDocumentation is available at [nextstrain.org/docs](https://nextstrain.org/docs).\n\n\n# Augur\n\n*Definition: One held to foretell events by omens.*\n\nAugur is the bioinformatics toolkit we use to track evolution from sequence and serological data.\nIt provides a collection of commands which are designed to be composable into larger processing pipelines.\nDocumentation for augur is available at [nextstrain.org/docs/bioinformatics](https://nextstrain.org/docs/bioinformatics).\n\n\n## Installation\n\nAugur is written in Python 3 and requires at least Python 3.4.\nIt's published on [PyPi](https://pypi.org) as [nextstrain-augur](https://pypi.org/project/nextstrain-augur), so you can install it with `pip` (or `pip3`) like so:\n\n    pip install nextstrain-augur\n\nYou can also install from a git clone or other copy of the source code by running:\n\n    pip install .\n\nIf your system has both Python 2 and Python 3 installed side-by-side, you may need to use `pip3` or `python3 -m pip` instead of just `pip` (which often defaults to Python 2 when both Python versions are installed).\n\nThis install depends on a fairly minimal set of external Python libraries. There are some\nfunctions in augur that require a larger set of dependencies. These can be installed via:\n\n    pip install .[full]\n\nAugur uses some common external bioinformatics programs which you'll need to install to have a fully functioning toolkit:\n\n* `augur align` requires [mafft](https://mafft.cbrc.jp/alignment/software/)\n\n* `augur tree` requires at least one of:\n   - [IQ-TREE](http://www.iqtree.org/) (used by default)\n   - [RAxML](https://sco.h-its.org/exelixis/web/software/raxml/) (optional alternative)\n   - [FastTree](http://www.microbesonline.org/fasttree/) (optional alternative)\n\n* Bacterial data (or any VCF usage) requires [vcftools](https://vcftools.github.io/)\n\nAlternatively, all these dependencies (as well as augur itself) can be installed via Conda by running:\n\n    conda env create -f environment.yml\n\nOnce installed, Conda the enviroment need to be activated whenever augur is to be used, by running:\n\n    conda activate augur\n\n## Usage\n\nAll of Augur's commands are accessed through the `augur` program.\nFor example, to infer ancestral sequences from a tree, you'd run `augur ancestral`.\nIf you've installed the `nextstrain-augur` package, you can just run `augur`.\nOtherwise, you can run `./bin/augur` from a copy of the source code.\n\n```\nusage: augur [-h] {parse,filter,mask,align,tree,refine,ancestral,translate,clades,traits,sequence-traits,titers,export,validate,version} ...\n\nAugur: A bioinformatics toolkit for phylogenetic analysis.\n\npositional arguments:\n  {parse,filter,mask,align,tree,refine,ancestral,translate,clades,traits,sequence-traits,titers,export,validate,version}\n    parse               Parse delimited fields from FASTA sequence names into\n                        a TSV and FASTA file.\n    filter              Filter and subsample a sequence set.\n    mask                Mask specified sites from a VCF file.\n    align               Align multiple sequences from FASTA or VCF.\n    tree                Build a tree using a variety of methods.\n    refine              Refine an initial tree using sequence metadata.\n    ancestral           Infer ancestral sequences based on a tree.\n    translate           Translate gene regions from nucleotides to amino\n                        acids.\n    clades              Assign clades to nodes in a tree based on amino-acid\n                        or nucleotide signatures.\n    traits              Infer ancestral traits based on a tree.\n    sequence-traits     Annotate sequences based on amino-acid or nucleotide\n                        signatures.\n    titers              Annotate a tree with actual and inferred titer\n                        measurements.\n    export              Export JSON files suitable for visualization with\n                        auspice.\n    validate            Validate a set of JSON files intended for\n                        visualization in auspice.\n    version             Print the version of augur.\n\noptional arguments:\n  -h, --help            show this help message and exit\n```\n\nFor more information on a specific command, you can run it with the `--help` option, for example, `augur tree --help`.\n\n\n## Development\n\nDevelopment of `augur` happens at <https://github.com/nextstrain/augur>.\n\nWe currently target compatibility with Python 3.4 and higher.  This may be\nincreased to in the future.\n\nVersions for this project from 3.0.0 onwards aim to follow the [Semantic\nVersioning rules](https://semver.org).\n\n### Running with local changes\n\nFrom within a clone of the git repository you can run `./bin/augur` to test your local changes without installing them.\n(Note that `./bin/augur` is not the script that gets installed by pip as `augur`; that script is generated by the `entry_points` configuration in `setup.py`.)\n\nYou can also install augur from source as an \"editable\" package so that your global `augur` command always uses your local source code copy:\n\n    pip install -e .[dev]\n\nThis is not recommended if you want to be able to compare output from a stable version of augur to a development version (e.g. comparing output of `augur` installed with pip and `./bin/augur` from your local source code).\n\n### Testing\n\nRun doctests and unit tests for augur from Python 3 with pytest from the top-level of the augur repository.\n\n    pytest -c pytest.python3.ini\n\nOr, run tests for augur from Python 2.\n\n    pytest -c pytest.python2.ini\n\nAs tests run on the development code in the augur repository, your environment should not have an existing augur installation that could cause a conflict in pytest.\n\n### Releasing\n\nNew releases are tagged in git using a [_signed_ tag][].  The `release` branch\nshould always point to the latest release tag.  Source and wheel (binary)\ndistributions are uploaded to [the nextstrain-augur project on\nPyPi](https://pypi.org/project/nextstrain-augur).\n\nThere is a `./devel/release` script which will prepare a new release from your\nlocal repository.  It ends with instructions for you on how to push the release\ncommit/tag/branch and how to upload the built distributions to PyPi.  You'll\nneed [a PyPi account][] and [twine][] installed to do the latter.\n\n[_signed_ tag]: https://git-scm.com/book/en/v2/Git-Tools-Signing-Your-Work\n[a PyPi account]: https://pypi.org/account/register/\n[twine]: https://pypi.org/project/twine\n\n### Travis CI\n\nBranches and PRs are tested by Travis CI jobs configured in `.travis.yml`.\n\nNew releases, via pushes to the `release` branch, trigger a new [docker-base][]\nbuild to keep the Docker image up-to-date.\n\n[docker-base]: https://github.com/nextstrain/docker-base\n\n### Building documentation\n\n[Documentation](https://nextstrain-augur.readthedocs.io) is built using [Sphinx](http://sphinx-doc.org/) and hosted on [Read The Docs](https://readthedocs.org/).\nVersions of the documentation for each augur release and git branch are available and preserved.\n\nBuilding the documentation locally is useful to test changes.\nFirst, make sure you have the development dependencies of augur installed:\n\n    pip install '.[dev]'\n\nThis installs packages listed in the `dev` section of `extras_require` in _setup.py_ (in addition to any normal augur dependencies if necessary).\n\nThen build the HTML output format by running:\n\n    make -C docs html\n\nYou can see other available formats by running:\n\n    make -C docs help\n\nTo update the API documentation after adding or removing an augur submodule, autogenerate a new API file as follows.\n\n    sphinx-apidoc -T -f -MeT -o docs augur\n\nSphinx caches built documentation by default, which is generally great, but can cause the sidebar of pages to be stale.  You can clean out the cache with:\n\n    make -C docs clean\n\n## License and copyright\n\nCopyright 2014-2019 Trevor Bedford and Richard Neher.\n\nSource code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.\n\n\n",
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