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        "author": "Simon J. Greenhill",
        "author_email": "simon@simon.net.nz",
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        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": "# treemaker\n\nA Python library for creating a Newick formatted tree from a set of classification strings (e.g. a taxonomy)\n\n[![Build Status](https://travis-ci.org/SimonGreenhill/treemaker.svg?branch=master)](https://travis-ci.org/SimonGreenhill/treemaker)\n[![Coverage Status](https://coveralls.io/repos/SimonGreenhill/treemaker/badge.svg?branch=master&service=github)](https://coveralls.io/github/SimonGreenhill/treemaker?branch=master)\n[![DOI](https://zenodo.org/badge/22704/SimonGreenhill/treemaker.svg)](https://zenodo.org/badge/latestdoi/22704/SimonGreenhill/treemaker)\n[![status](http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23/status.svg)](http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23)\n\n```treemaker``` is a Python library to convert a text-based classification schema into a Newick file for use in phylogenetic and bioinformatic programs.\n\nResearch in linguistics or cultural evolution often produces or uses tree taxonomies or classifications. However, these are usually not in a format readily available for use in programs that can understand and manipulate trees. For example, the global taxonomy of languages published by the [Ethnologue](https://www.ethnologue.com/) classifies languages into families and subgroups using a taxonomy string e.g. the language [Kalam](https://www.ethnologue.com/language/kmh) is classified as \"Trans-New Guinea, Madang, Kalam-Kobon\", while [Mauwake](https://www.ethnologue.com/language/mhl) is classified as \"Trans-New Guinea, Madang, Croisilles, Pihom\", and [Kare](https://www.ethnologue.com/language/kmf) is \"Trans-New Guinea, Madang, Croisilles, Kare\". This classification indicates that while all these languages are part of the Madang subgroup of the Trans-New Guinea language family, Kare and Mauwake are more closely related (as they belong to the Croisilles subgroup).\n\nOther publications use a tabular indented format to demarcate relationships, such as the example in Figure 1 from Stephen Wurm's classification of his proposed Yele-Solomons language phylum (Wurm 1975).\n\nBoth the taxonomy string and tabular format however are hard to load into software packages that can analyse, compare, visualise and manipulate trees. ```treemaker``` aims to make this easy by converting taxonomic data into [Newick](https://en.wikipedia.org/wiki/Newick_format) and Nexus (Maddison 1997) formats commonly used by phylogenetic manipulation programs.\n\n## Converting a Taxonomy to a Tree:\n\n```treemaker``` can convert a text file with a taxonomy to a tree. These taxonomies can easily be obtained from Ethnologue or manually entered, such as this example from Wurm's (outdated) classification of Yele-Solomons in Figure 1:\n\n```text\nBilua       Yele-Solomons, Central Solomon\nBaniata     Yele-Solomons, Central Solomon\nLavukaleve  Yele-Solomons, Central Solomon\nSavosavo    Yele-Solomons, Central Solomon\nKazukuru    Yele-Solomons, Kazukuru\nGuliguli    Yele-Solomons, Kazukuru\nDororo      Yele-Solomons, Kazukuru\nYele        Yele-Solomons\n```\n\n``treemaker`` can then generate a Newick representation:\n\n```text\n((Baniata,Bilua,Lavukaleve,Savosavo),(Dororo,Guliguli,Kazukuru),Yele);\n```\n\n...which can then be loaded into phylogenetic programs to visualise or manipulate as in Figure 2.\n\n```treemaker``` has been used to enable the analyses in (Bromham et al. 2018), and a number of forthcoming articles.\n\n\n![Example of a language taxonomy in indented format from Wurm (1975).](wurm1975.png)\n\n![Tree visualisation of the relationships between the putative Yele-Solomons languages.](tree.png)\n\n\n## Installation:\n\nInstallation is only a pip install away:\n\n```shell\npip install treemaker\n```\n\nOr from git:\n\n```shell\ngit clone https://github.com/SimonGreenhill/treemaker/ treemaker\ncd treemaker\npython setup.py install\n```\n\n## Usage: Command line:\n\nBasic usage: \n\n```shell\n> treemaker\n\nusage: treemaker [-h] [-o OUTPUT] [-m {nexus,newick}] [--labels] input\n```\n\ne.g. Given a text file:\n\n```\nLangA   Indo-European, Germanic\nLangB   Indo-European, Germanic\nLangC   Indo-European, Romance\nLangD   Indo-European, Anatolian\n```\n\n... then you can build a taxonomy/classification tree from that as follows:\n\n```shell\n> treemaker classification.txt\n(LangD,(LangA,LangB),LangC);\n\n# with nodelabels:\n> treemaker --labels classification.txt\n(LangD,(LangA,LangB)Germanic,LangC)Indo-European;\n\n> treemaker -m nexus classification.txt\n\n#NEXUS\n\nbegin trees;\n   tree root = (LangD,(LangA,LangB),LangC);\nend;\n```\n\nTo write to file:\n\n```shell\n> treemaker classification.txt\n(LangD,(LangA,LangB),LangC);\n\n> treemaker classification.txt -o classification.nex\n```\n\n\n## Usage: Library:\n\n```python\nfrom treemaker import TreeMaker\n```\n\n### generate a tree manually:\n\n```python\nfrom treemaker import TreeMaker\n\nt = TreeMaker()\nt.add('A1', 'family a, subgroup 1')\nt.add('A2', 'family a, subgroup 2')\nt.add('B1a', 'family b, subgroup 1')\nt.add('B1b', 'family b, subgroup 1')\nt.add('B2', 'family b, subgroup 2')\n\nprint(t.write())\n```\n\n### Add from a list:\n\n```python\nfrom treemaker import TreeMaker\n\ntaxa = [\n    ('A1', 'family a, subgroup 1'),\n    ('A2', 'family a, subgroup 2'),\n    ('B1a', 'family b, subgroup 1'),\n    ('B1b', 'family b, subgroup 1'),\n    ('B2', 'family b, subgroup 2'),\n]\n\nt = TreeMaker()\nt.add_from(taxa)\n\nprint(t.write())\n\n```\n\n## API Documentation:\n\nThe API is [documented here](https://simongreenhill.github.io/treemaker/build/html/index.html).\n\n## Running treemaker's tests:\n\nTo run treemaker's tests simply run:\n\n```shell\n> make test\n# or\n> python setup.py test\n# or\n> python treemaker/test_treemaker.py\n```\n\n\n## Version History:\n\n* v1.3: add nodelabels support, add some rudimentary input checking.\n\n## Support:\n\nFor questions on how to use or update this, feel free to [open an issue](https://github.com/SimonGreenhill/treemaker/issues). I'll get to it as soon as I can. \n\n## References:\n\n* Bromham, Lindell, Xia Hua, Marcel Cardillo, Hilde Schneemann, & Simon J. Greenhill. 2018. \u201c[Parasites and Politics: Why Cross-Cultural Studies Must Control for Relatedness, Proximity and Covariation](https://doi.org/10.1098/rsos.181100).\u201d Open Science 5 (8). https://doi.org/10.1098/rsos.181100.\n* Maddison, D R, D L Swofford, & Wayne P. Maddison. 1997. \u201c[Nexus: An Extensible File Format for Systematic Information](https://doi.org/10.1093/sysbio/46.4.590).\u201d Systematic Biology 46 (4): 590\u2013621. https://doi.org/10.1093/sysbio/46.4.590.\n* Wurm, S. A. 1975. \u201c[The East Papuan Phylum in General](https://doi.org/http://dx.doi.org/10.15144/PL-C38).\u201d In New Guinea Area Languages and Language Study: Papuan Languages and the New Guinea Linguistic Scene, edited by S. A. Wurm. Canberra: Pacific Linguistics. https://doi.org/http://dx.doi.org/10.15144/PL-C38.\n\n\n",
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