{
    "info": {
        "author": "EnteroBase development team",
        "author_email": "zhemin.zhou@warwick.ac.uk",
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        "description": "# GrapeTree\n\n[![Build Status](https://travis-ci.org/achtman-lab/GrapeTree.svg?branch=master)](https://travis-ci.org/achtman-lab/GrapeTree)\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Docs Status](https://readthedocs.org/projects/enterobase/badge/)](http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html)\n\n**[Click here for the live demo of GrapeTree!](https://achtman-lab.github.io/GrapeTree/MSTree_holder.html)**\n\nGrapeTree is an integral part of EnteroBase and we advise that you use GrapeTree\nthrough EnteroBase for the best results. However, many people have asked for a\nstand-alone GrapeTree version that they could use offline or integrate into the\nother applications.\n\nThe stand-alone version emulates the EnteroBase version through a lightweight\nwebserver running on your local computer.  You will be interacting with the\nprogram as you would in EnteroBase; through a web browser. We recommend\n[Google Chrome](https://www.google.com/chrome/index.html) for best results.\n\n**For detailed help please see: [http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html](http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html)**\n\n**For a formal description, please see the accepted manuscript in Genome Research: [https://doi.org/10.1101/gr.232397.117\n](https://doi.org/10.1101/gr.232397.117\n)**\n\n## Installing and Running GrapeTree\nThere are number of different ways to interact with GrapeTree, for **best results install via pip** :\n\n```\npip install grapetree\ngrapetree\n```\n\n**We also have ready-made binaries for download here: [https://github.com/achtman-lab/GrapeTree/releases](https://github.com/achtman-lab/GrapeTree/releases)**\n\n**Running on Mac: Download GrapeTree_mac.zip**\n\nYou will need to unzip GrapeTree_mac.zip (just double click). Inside there will\nbe an app you can drag into your Applications folder. You may be warned about\nSecurity settings, if you right click on the GrapeTree app and then click \"Open\"\nit should be fine.\n\n**Running on Windows: Download GrapeTree_win.zip**\n\nOnce downloaded, you will need to untzip GrapeTree_win.zip and then open the\nextracted folder and  run GrapeTree_win.exe. When you run it the first time on\nwindows you might get a prompt about security. On Windows 10, click the small\ntext: \"More info\", and then the button \"Run Anyway\".\n\n**Running from Source code**\n\nGrapeTree requires [Python 2.7](https://www.python.org/downloads/release/python-2712/) or [Python 3.6](https://www.python.org/downloads/release/python-360/)\nand some additional python modules (listed in requirements.txt). The easiest way\nto install these modules is with pip:\n\n```\npip install -r requirements.txt\nchmod +x binaries/\n```\nOn Linux or MacOSX you need to make sure the binaries in binaries/ can be\nexecuted. To run GrapeTree;\n\n1. Navigate to the directory where you installed GrapeTree.\n1. Run it through python as below.\n\n```\n\\GrapeTree>python grapetree.py\n * Running on http://127.0.0.1:8000/ (Press CTRL+C to quit)\n```\n\nThe program will automatically open your web browser and you will see the\nGrapeTree Splash Screen. If at anytime you want to restart the page you can\nvisit [http://localhost:8000](http://localhost:8000) in your web browser. To\nview a tree (newick or Nexus) or create a tree from an allele profile, just drag\nand drop the file into the browser window.\n\n### Configuration\nRuntime behaviour can be configured in grapetree/config.py.\n\nDevelopers may wish to look at the [JavaScript documentation](https://achtman-lab.github.io/GrapeTree/documentation/developer/index.html) (JSDoc).\n\n### Tests\nTo run tests, run pytests in the top level directory.\n```\npytest\n\n```\n\n## Usage - Command line module for generating Trees\n```\n>grapetree -h\nusage: MSTrees.py [-h] --profile FNAME [--method TREE] [--matrix MATRIX_TYPE]\n                  [--recraft] [--missing HANDLER] [--wgMLST]\n                  [--heuristic HEURISTIC] [--n_proc NUMBER_OF_PROCESSES]\n                  [--check]\n\nFor details, see \"https://github.com/achtman-lab/GrapeTree/blob/master/README.md\".\nIn brief, GrapeTree generates a NEWICK tree to the default output (screen)\nor a redirect output, e.g., a file.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --profile FNAME, -p FNAME\n                        [REQUIRED] An input filename of a file containing MLST or SNP character data, \n                        OR a fasta file containing aligned sequences.\n  --method TREE, -m TREE\n                        \"MSTreeV2\" [DEFAULT]\n                        \"MSTree\"\n                        \"NJ\": FastME V2 NJ tree\n                        \"RapidNJ\": RapidNJ for very large datasets\n                        \"distance\": p-distance matrix in PHYLIP format.\n  --matrix MATRIX_TYPE, -x MATRIX_TYPE\n                        \"symmetric\": [DEFAULT: MSTree and NJ]\n                        \"asymmetric\": [DEFAULT: MSTreeV2].\n  --recraft, -r         Triggers local branch recrafting. [DEFAULT: MSTreeV2].\n  --missing HANDLER, -y HANDLER\n                        ONLY FOR symmetric DISTANCE MATRIX.\n                        0: [DEFAULT] ignore missing data in pairwise comparison.\n                        1: Remove column with missing data.\n                        2: treat data as an allele.\n                        3: Absolute number of allelic differences.\n  --heuristic HEURISTIC, -t HEURISTIC\n                        Tiebreak heuristic used only in MSTree and MSTreeV2\n                        \"eBurst\" [DEFAULT: MSTree]\n                        \"harmonic\" [DEFAULT: MSTreeV2]\n  --n_proc NUMBER_OF_PROCESSES, -n NUMBER_OF_PROCESSES\n                        Number of CPU processes in parallel use. [DEFAULT]: 5.\n  --check, -c           Only calculate the expected time/memory requirements.\n```\nNOTE:\n* Detailed descriptions for [--matrix](https://github.com/achtman-lab/GrapeTree/blob/master/documentation/asymmetricDistances.pdf), [--recraft](https://github.com/achtman-lab/GrapeTree/blob/master/documentation/branchRecrafting.pdf) and [--heuristic](https://github.com/achtman-lab/GrapeTree/blob/master/documentation/tiebreak.pdf)\n\n## Inputs\n#### profile\nThe profile file is a tab-delimited text file.\n\nFollow an example here: https://github.com/achtman-lab/GrapeTree/blob/master/examples/simulated_data.profile\n```\n#Strain\tGene_1\tGene_2\tGene_3\tGene_4\tGene_5\tGene_6\tGene_7\t...\n0\t1\t1\t1\t1\t1\t1\t1\t...\n1\t1\t1\t1\t1\t1\t1\t1\t...\n2\t1\t2\t2\t2\t2\t2\t2\t...\n...\n```\nThe first row is required and represents column labels. It has to start with a '#'. Collumn labels that start with a '#' are treated as comments and will not be used in downstream analysis. The first column needs to be unique identifiers for strains.\nEach of the remaining rows presents a different strain.\n\nUse '-' or '0' to represent missing alleles. \n\n#### Aligned FASTA\nAn aligned FASTA file contains multiple sequences of the same length in FASTA format. Many sequence alignment tools, e.g., MAFFT and MUSCLE, use FASTA as a default format for their outputs. \n\nFind an example here: http://wwwabi.snv.jussieu.fr/public/Clustal2Dna/fastali.html\n\nNote that GrapeTree supports only p-distance for the moment.  \n\n#### metadata\nThe metadata file is either a tab-delimited or a comma-delimited text file. This is only used for tree presentation in the standardalone version.\n\nFollow an example here: https://github.com/achtman-lab/GrapeTree/blob/master/examples/simulated_data.metadata.txt\n```\nID\tCountry\tYear\n0\tChina\t1983\n1\tChina\t1984\n...\n```\nThe first row is required and describes the labels of the columns. If a column labeled with \"ID\" presents, it will be used to correlate metadata with profiles, otherwise the first column will be used.\n\n## outputs\n#### tree\nThe tree is described in NEWICK format. https://en.wikipedia.org/wiki/Newick_format\n\n#### distance matrix\nUse the option '--method distance' to generate a distance matrix without calculating the tree.\nThe matrix is presented in PHYLIP format. http://evolution.genetics.washington.edu/phylip/doc/distance.html\n\n## Command line examples\n#### MSTree V2\n```\npython grapetree.py -p examples/simulated_data.profile -m MSTreeV2\n```\n#### NJ tree\n```\npython grapetree.py -p examples/simulated_data.profile -m NJ\n```\n#### distance matrix\n```\npython grapetree.py -p examples/simulated_data.profile -m distance\n```\n\n## License\nCopyright Warwick University This program is free software: you can\nredistribute it and/or modify it under the terms of the GNU General Public\nLicense as published by the Free Software Foundation, either version 3 of the\nLicense, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful, but without\nany warranty; without even the implied warranty of merchantability or fitness\nfor a particular purpose. See the GNU General Public License for more\ndetails.\n\nYou should have received a copy of the GNU General Public License along with\nthis program. If not, see <http://www.gnu.org/licenses/>.\n\n## External programs\nDetailed information for the standard NJ implemented in FastME V2: http://www.atgc-montpellier.fr/fastme/\n\n## Citation\nEnteroMSTree - GrapeTree has been formally accepted by Genome Research. Please use the citation:\n\nZ Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico,\nM Achtman (2018) \"GrapeTree: Visualization of core genomic relationships among \n100,000 bacterial pathogens\", Genome Res; doi:\n[https://doi.org/10.1101/gr.232397.117](https://doi.org/10.1101/gr.232397.117)",
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