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Download and Install

Linux

Using Conda (no sudo required)

  1. Installing ETE using the Anaconda/Miniconda environment
  2. # Install Minconda  (you can ignore this step if you already have Anaconda/Miniconda)
    wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
    bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
    export PATH=~/anaconda_ete/bin:$PATH;
    
    # Install ETE
    conda install -c etetoolkit ete3 ete3_external_apps
    
    # Check installation
    ete3 version
    ete3 build check
  3. Run the following line to activate Anaconda before using ETE:
    # Activate the environment 
    export PATH=~/anaconda_ete/bin:$PATH
    
    Tip: you can add the line to your .bashrc to make it permanent

Native

  1. Install dependencies: python-qt4, python-lxml, python-six and python-numpy

    (PyQt4 and lxml are optional, required for tree drawing operations and PhyloXML/NexML format parsing respectively. You can still install ETE without them.)

    • In Ubuntu, Mint and other Debian based distributions (APT)
    • sudo apt-get install python-numpy python-qt4 python-lxml python-six
    • In CentOS, Fedora, etc (YUM)
    • sudo yum install PyQt4.x86_64 numpy.x86_64 python-lxml.x86_64 python-six.noarch
  2. Install/Upgrade ETE using PIP
    pip install --upgrade ete3
    or using EasyInstall
    easy_install -U ete3
    or from the sources: Download latest version from PyPI and execute:
    python setup.py install 
  3. Compile external tools

    This is an optional step, required only by ete-build and ete-evol. The Python API does not require external tools.

    ete3 upgrade-external-tools

Mac OS X

Using Conda (recommended)

  1. Install ETE using the Anaconda/Miniconda Python distribution

    # Install Minconda  (you can ignore this step if you already have Anaconda/Miniconda)
    curl -L 'http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh' -o Miniconda-latest-MacOSX-x86_64.sh
    bash Miniconda-latest-MacOSX-x86_64.sh -b -p ~/anaconda_ete/
    export PATH=~/anaconda_ete/bin:$PATH;
                
    # Install ETE and external tools 
    conda install -c etetoolkit ete3 ete3_external_apps 
    
    # Check installation
    ete3 version
    ete3 build check
  2. Run the following line to activate Anaconda before using ETE:
    # Activate the environment 
    export PATH=~/anaconda_ete/bin:$PATH
    
    Tip: you can add the line to your .bashrc to make it permanent

XQuartz

Note that graphical features in ETE require XQuartz to be installed.

Older versions (ete2)

For compatibility and reproducibility reasons, the older ete2 version of the API is still available and can be installed independently from ete3 (both versions can coexist). Use pip install --upgrade ete2 to install it.