Metadata-Version: 1.1
Name: grapetree
Version: 1.2.1
Summary: Web interface of GrapTree, which is a program for phylogenetic analysis.
Home-page: https://github.com/martinSergeant/EnteroMSTree
Author: EnteroBase development team
Author-email: zhemin.zhou@warwick.ac.uk
License: UNKNOWN
Description: # EnteroMSTree - GrapeTree

        

        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: https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree**

        

        **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 to 

        download the software here: [https://github.com/martinSergeant/EnteroMSTree/releases](https://github.com/martinSergeant/EnteroMSTree/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** 

        

        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:

        

        ```

        #!bash

        

        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. 

        

        ```

        #!bash

        

        \GrapeTree>python main.py

         * Running on http://127.0.0.1:8000/ (Press CTRL+C to quit)

        ```

        

        **Running GrapeTree with no installation**

        

        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 

        

        ### Tests

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

        ```bash

        pytest

        

        ```

        

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

        ### parameters :

                profile: input file. Can be either profile or fasta. Headings start with an '#' will be ignored. 

                method: MST or NJ

                matrix_type: asymmetric or symmetric

                edge_weight: harmonic or eBurst

                neighbor_branch_reconnection: T or F

            

        ### Outputs :

                A string of a NEWICK tree

            

        ### Examples :

                To run a Balanced Spanning Arborescence (BSA), use :

                backend(profile=<filename>, method='MST', matrix_type='asymmetric', edge_weight='harmonic', neighbor_branch_reconnection='T')

            

                OR simply

                backend(profile=<filename>)

                

                To run a standard minimum spanning tree :

                backend(profile=<filename>, method='MST', matrix_type='symmetric', edge_weight='eBurst', neighbor_branch_reconnection='F')

                

                To run a NJ tree (using FastME 2.0) :

                backend(profile=<filename>, method='NJ')

            

        ### Can also be called in command line:

                BSA: MSTrees.py profile=<filename> method=MST matrix_type=asymmetric edge_weight=harmonic neighbor_branch_reconnection=T

                MST: MSTrees.py profile=<filename> method=MST matrix_type=symmetric edge_weight=eBurst neighbor_branch_reconnection=F

                NJ:  MSTrees.py profile=<filename> method=NJ

        

        

        ## 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:

        https://www.biorxiv.org/content/early/2017/11/09/216788

        

        An extended citation could be:

        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

        
Keywords: visulisation bioinformatics microbial genomics
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
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
