Metadata-Version: 1.1
Name: grapetree
Version: 1.3.2
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

        =========

        

        Click here for the `live demo of GrapeTree! <https://achtman-lab.github.io/GrapeTree/MSTree_holder.html>`_ 

        **************************************************************************************************************

        |Build Status| |License| |Doc Status|

        

        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

        

        **For a formal description, please see the preprint:** https://www.biorxiv.org/content/early/2017/11/09/216788

        

        Installing and Running GrapeTree

        --------------------------------

        There are number of different ways to interact with GrapeTree, the easiest is to 

        install with pip or download the software here: https://github.com/achtman-lab/GrapeTree/releases

        

        **Installing with pip**

        

        .. code-block::

        

           pip install grapetree

           grapetree

        

        **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** 

        

        EnteroMSTree - 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:

        

        .. code-block::

        

           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;

        

        #. Navigate to the directory where you installed GrapeTree. 

        #. Run it through python as below. 

        

        .. code-block::

        

           \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 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 (JSDoc) <https://achtman-lab.github.io/GrapeTree/documentation/developer/index.html>`_.

        

        Tests

        -----

        To run tests, run pytests in the top level directory.

        

        .. code-block::

        

           pytest

        

        Usage - Command line module for generating Trees - MSTrees.py

        -------------------------------------------------------------

        

        .. code-block::

        

           usage: MSTrees.py [-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          Use when > 20 % of values in the input are missing.

          --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 

        --------

        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

        

        .. |Build Status| image:: https://travis-ci.org/achtman-lab/GrapeTree.svg?branch=master

            :target: https://travis-ci.org/achtman-lab/GrapeTree

            :alt: Build status

        

        .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg

            :target: https://www.gnu.org/licenses/gpl-3.0

            :alt: GPLv3

        

        .. |Doc status| image:: https://readthedocs.org/projects/enterobase/badge/

            :target: http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html

            :alt: Build status of documentation

        
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
