Metadata-Version: 2.1
Name: phylosuite
Version: 2.0.dev5
Summary: From sequence to tree and time: Phylogenetics and molecular dating made easy with PhyloSuite
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+)
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
Requires-Dist: pyparsing (==3.0.7)
Requires-Dist: Pillow (==8.4.0)
Requires-Dist: numpy (==1.19.5)
Requires-Dist: netCDF4 (==1.5.6)
Requires-Dist: biopython (==1.76)
Requires-Dist: python-dateutil
Requires-Dist: suds-py3
Requires-Dist: PyQt5 (==5.10.1)
Requires-Dist: psutil
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Requires-Dist: pandas (==1.1.5)
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Requires-Dist: DendroPy (==4.4.0)
Requires-Dist: kaleido (==0.2.1) ; platform_system == "Darwin"
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Requires-Dist: kaleido (==0.2.1) ; platform_system == "Linux"
Requires-Dist: statsmodels (==0.12.2) ; platform_system == "Linux"
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Requires-Dist: statsmodels (==0.12.2) ; platform_system == "Windows"
Requires-Dist: matplotlib (==3.3.4) ; platform_system == "Windows"


# 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>)



