Installation

1. Install compiled PhyloSuite

Installers for all platforms can be downloaded from https://github.com/dongzhang0725/PhyloSuite/releases.

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_Win64/32.rar, unzip it, and run PhyloSuite directly from this folder.

1.2. Mac OSX & 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:

1 2	cd [PhyloSuite_installation_path]/PhyloSuite ./PhyloSuite

If you encounter an error of “permission denied”, try to use the following command:

1	bash [PhyloSuite_installation_path]/assign_permission.sh

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 18.04.6 LTS) and Mac OSX (macOS Sierra version 10.12.3 and above).
We strongly encourage you to use conda to install PhyloSuite in Linux (see section 3), especially for version 1.2.3.

2. Install using pip

First, Python (version 3.6) should be installed and added to the environment variable in your computer. Then open the terminal and type:

1	pip install PhyloSuite==1.2.3rc3

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:

1	PhyloSuite

3. Install using conda

First, Miniconda3 (https://docs.conda.io/en/latest/miniconda.html) should be installed and added to the environment variable in your computer. Then open the terminal and create an evironment for python 3.6:

1	conda create -n py367 python=3.6.7

Now you can install PhyloSuite using "py367" environment:

1	conda activate py367 pip install PhyloSuite==1.2.3rc3

It will take some time to install. If it installs successfully, PhyloSuite will be installed into [Miniconda_installation_path]/envs/py367/bin folder and will be automatically added to the environment variables. Then open the terminal again and type:

1	conda activate py367 # execute this if you are not in py367 environment PhyloSuite

If the above pip or conda 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.