Metadata-Version: 1.1
Name: grapetree
Version: 1.3.8
Summary: Web interface of GrapeTree, which is a program for phylogenetic analysis.
Home-page: https://github.com/achtman-lab/GrapeTree
Author: EnteroBase development team
Author-email: zhemin.zhou@warwick.ac.uk
License: UNKNOWN
Description: # GrapeTree
        
        [![Build Status](https://travis-ci.org/achtman-lab/GrapeTree.svg?branch=master)](https://travis-ci.org/achtman-lab/GrapeTree)
        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
        [![Docs Status](https://readthedocs.org/projects/enterobase/badge/)](http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html)
        
        **[Click here for the live demo of GrapeTree!](https://achtman-lab.github.io/GrapeTree/MSTree_holder.html)** 
        
        GrapeTree is an integral part of EnteroBase and we advise that you use GrapeTree
        through EnteroBase for the best results. However, many people have asked for a 
        stand-alone GrapeTree version that they could use offline or integrate into the
        other applications. 
        
        The stand-alone version emulates the EnteroBase version through a lightweight 
        webserver running on your local computer.  You will be interacting with the 
        program as you would in EnteroBase; through a web browser. We recommend 
        [Google Chrome](https://www.google.com/chrome/index.html) for best results.
        
        **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)**
        
        **For a formal description, please see the preprint: [https://www.biorxiv.org/content/early/2017/11/09/216788](https://www.biorxiv.org/content/early/2017/11/09/216788)**
        
        ## Installing and Running GrapeTree
        There are number of different ways to interact with GrapeTree, for **best results install via pip** :
        
        ```
        pip install grapetree
        grapetree
        ```
        
        **We also have ready-made binaries for download here: [https://github.com/achtman-lab/GrapeTree/releases](https://github.com/achtman-lab/GrapeTree/releases)**
        
        **Running on Mac: Download GrapeTree_mac.zip**
        
        You will need to unzip GrapeTree_mac.zip (just double click). Inside there will 
        be an app you can drag into your Applications folder. You may be warned about 
        Security settings, if you right click on the GrapeTree app and then click "Open" 
        it should be fine. 
        
        **Running on Windows: Download GrapeTree_win.zip**
        
        Once downloaded, you will need to untzip GrapeTree_win.zip and then open the 
        extracted folder and  run GrapeTree_win.exe. When you run it the first time on 
        windows you might get a prompt about security. On Windows 10, click the small 
        text: "More info", and then the button "Run Anyway". 
        
        **Running from Source code** 
        
        GrapeTree requires [Python 2.7](https://www.python.org/downloads/release/python-2712/) 
        and some additional python modules (listed in requirements.txt). The easiest way
        to install these modules is with pip:
        
        ```
        pip install -r requirements.txt
        chmod +x binaries/
        ```
        On Linux or MacOSX you need to make sure the binaries in binaries/ can be
        executed. To run GrapeTree;
        
        1. Navigate to the directory where you installed GrapeTree. 
        1. Run it through python as below. 
        
        ```
        \GrapeTree>python main.py
         * Running on http://127.0.0.1:8000/ (Press CTRL+C to quit)
        ```
        
        The program will automatically open your web browser and you will see the 
        GrapeTree Splash Screen. If at anytime you want to restart the page you can 
        visit [http://localhost:8000](http://localhost:8000) in your web browser. To 
        view a tree (newick or Nexus) or create a tree from an allele profile, just drag
        and drop the file into the browser window. 
        
        ### Configuration
        Runtime behaviour can be configured in grapetree/config.py. 
        
        Developers may wish to look at the [JavaScript documentation](https://achtman-lab.github.io/GrapeTree/documentation/developer/index.html) (JSDoc).
        
        ### Tests
        To run tests, run pytests in the top level directory.
        ```
        pytest
        
        ```
        
        ## Usage - Command line module for generating Trees
        ```
        usage: grapetree [-h] --profile PROFILE [--method METHOD]
                          [--matrix MATRIX_TYPE] [--recraft]
                          [--missing HANDLE_MISSING] [--wgMLST]
                          [--heuristic HEURISTIC] [--n_proc N_PROC] [--check]
        
        Parameters for command line version of GrapeTree. 
        You can drag the Newick output into the web interface. 
        
        optional arguments:
          -h, --help            show this help message and exit
          --profile PROFILE, -p PROFILE
                                A file contains either MLST / SNP profiles or multile aligned sequences in fasta format.
          --method METHOD, -m METHOD
                                backend algorithms to call. Allowed values are "MSTreeV2" [default], "MSTree" and "NJ"
          --matrix MATRIX_TYPE, -x MATRIX_TYPE
                                Either "symmetric" [default for MSTree and NJ] 
                                or "asymmetric" [default for MSTreeV2]. 
          --recraft, -r         Allows local branch recrafting after tree construction. Default in MSTreeV2. 
          --missing HANDLE_MISSING, -y HANDLE_MISSING
                                Alternative ways of handling missing data.
                                0: missing data are ignored in pairwise comparisons [default]. 
                                1: Columns that have missing data are ignored in the whole analysis. 
                                2: missing data are treated as a special value (allele). 
                                3: Naive counting of absolute differences between profiles. 
          --wgMLST, -w          Experimental option for a better support of wgMLST schemes.
          --heuristic HEURISTIC, -t HEURISTIC
                                Tiebreak rules between co-optimal edges. Only used in MSTree [default: eBurst] and MSTreeV2 [default: harmonic]
          --n_proc N_PROC, -n N_PROC
                                Number of processes. Default: 5. 
          --check, -c           Do not calculate the tree but only show the expected time/memory consumption. 
        ```
        
        
        ## License
        Copyright Warwick University This program is free software: you can
        redistribute it and/or modify it under the terms of the GNU General Public
        License as published by the Free Software Foundation, either version 3 of the
        License, or (at your option) any later version.
        
        This program 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 General Public License for more
        details.
        
        You should have received a copy of the GNU General Public License along with
        this program. If not, see <http://www.gnu.org/licenses/>.
        
        
        ## Citation 
        EnteroMSTree - GrapeTree has not been formally published yet. If
        you use GrapeTree please cite the preprint:
        
        Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico,
        M Achtman (2017) "GrapeTree: Visualization of core genomic relationships
        among 100,000 bacterial pathogens", bioRxiv 216788; doi:
        [https://doi.org/10.1101/216788](https://doi.org/10.1101/216788)
        
Keywords: bioinformatics,microbial,genomics,MLST,visulisation
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
