PKG-INFO

Metadata-Version: 2.1
Name: PhyloSuite
Version: 1.2.3rc2
Summary: A desktop platform for streamlined molecular sequence data management and state of the art evolutionary phylogenetics studies.
Home-page: https://github.com/dongzhang0725/PhyloSuite
Author: Dong Zhang
Author-email: dongzhang0725@gmail.com
License: GNU Affero General Public License v3 or later (AGPLv3+)
Description: 
        # PhyloSuite
        PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. It combines the functions of two previous tools: MitoTool (https://github.com/dongzhang0725/MitoTool) and BioSuite (https://github.com/dongzhang0725/BioSuite).
        
        The interface and the main functions of PhyloSuite.  
        
        ![main_functions.jpg](https://github.com/dongzhang0725/PhyloSuite_tutorial/blob/master/images/main_functions.jpg?raw=true)
        
        The workflow diagram of PhyloSuite.  
        
        ![flowchart.jpg](https://github.com/dongzhang0725/PhyloSuite_tutorial/blob/master/images/flowchart.jpg?raw=true)
        
        The summary of flowchart and references of used programs.  
        
        ![flowchart_summary.jpg](https://github.com/dongzhang0725/PhyloSuite_tutorial/blob/master/images/flowchart_summary.jpg?raw=true)
        
        ## Homepage
        
        https://dongzhang0725.github.io or http://phylosuite.jushengwu.com/ (China)
        
        ## Installation
        
        ### 1. Install compiled PhyloSuite 
        
        Installers for all platforms can be downloaded from https://github.com/dongzhang0725/PhyloSuite/releases.
        
        <a id="download" href="https://github.com/dongzhang0725/PhyloSuite/releases"><i class="fa fa-download"></i><span> Download Now</span> </a>
        
        <a id="download" href="http://phylosuite.jushengwu.com/dongzhang0725.github.io/installation/#Chinese_download_link"><i class="fa fa-download"></i><span> Chinese download links</span> </a>
        
        #### 1.1. Windows
        Windows 7, 8 and 10 are supported, just double click the `PhyloSuite_xxx_win_setup.exe` to install, and run “PhyloSuite.exe” file after the installation. If the installation fails, download `PhyloSuite_xxx_Win.rar`, unzip it, and run PhyloSuite directly from this folder.
        
        #### 1.2. Mac OSX &&nbsp;Linux
        Unzip `PhyloSuite_xxx_Mac.zip/PhyloSuite_xxx_Linux.tar.gz` to anywhere you like, and double click “PhyloSuite” (in PhyloSuite folder) to start, or use the following command: 
        
        ```
        cd path/to/PhyloSuite
        ./PhyloSuite
         ```
        If you encounter an error of "permission denied", try to use the following command:
        
        ```
        chmod -R 755 path/to/PhyloSuite(folder)
         ```
        
        <span style="color:red">Note that both 64 bit and 32 bit Windows is supported (Windows 7 and above), whereas only 64 bit has been tested in Linux (Ubuntu 14.04.1 and above) and Mac OSX (macOS Sierra version 10.12.3 and above).</span>
        
        ### 2. Install using pip
        
        First, Python (version higher than 3.6) should be installed and added to the environment variable in your computer. Then open the terminal and type:
        
        ```
        pip install PhyloSuite
        ```
        
        It will take some time to install. If it installs successfully, PhyloSuite will be automatically added to the environment variables. Then open the terminal again and type:
         ```
         PhyloSuite
         ```
        
        If the above `pip` command failed to install PhyloSuite, you can use compiled PhyloSuite (see `section 1`) or find and download the source codes here (https://pypi.org/project/PhyloSuite/#files or https://github.com/dongzhang0725/PhyloSuite), and install it manually.
        
        ### 3. Install manually
        
        Similarly, Python (version higher than 3.6) should be pre-installed and added to the environment variable in your computer. If it is, then download the PhyloSuite from github, either using `git clone https://github.com/dongzhang0725/PhyloSuite.git` or use the `Clone or download`-->`Download ZIP` button in https://github.com/dongzhang0725/PhyloSuite.
        After that, change your directory to the `PhyloSuite` folder that contains the `setup.py` file, then type:
        
        ```
        python setup.py install
        ```
        
        ## Examples
        
        https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/example.zip
        
        ## Bug report
        
        [Google group](https://groups.google.com/forum/#!forum/phylosuite), [Github issue](https://github.com/dongzhang0725/PhyloSuite/issues) or send email to dongzhang0725@gmail.com.
        
        ## Citation
        Zhang, D., F. Gao, I. Jakovlić, H. Zou, J. Zhang, W.X. Li, and G.T. Wang, PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 2020. 20(1): p. 348–355. DOI: 10.1111/1755-0998.13096. (Download as: <a href="https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/PhyloSuite/PhyloSuite_citation.ris">RIS</a>   <a href="https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/PhyloSuite/PhyloSuite_citation.xml">XML</a>   <a href="https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/PhyloSuite/PhyloSuite_citation.enw">ENW</a>)
        
        
Platform: Linux; MacOS X; Windows
Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: User Interfaces
Requires-Python: >=3.6.0, <=3.7.0
Description-Content-Type: text/markdown