Download

Please pick the right .tar.gz file to download from the list.

📦 orthofinder-linux-intel-3.1.0.tar.gz

Older versions of OrthoFinder can be downloaded from here.
For a full list of OrthoFinder before v3.0.1b1, see the GitHub Releases.

Installation

The easiest way to install OrthoFinder is using conda.

conda create -n of3_env python=3.10
conda activate of3_env
conda install orthofinder

Alternatively, you could install via github, or download the source code and install locally.

Install via github

python3 -m venv of3_env 
. of3_env/bin/activate
pip install git+https://github.com/OrthoFinder/OrthoFinder.git

Install locally from source code

The following commands provide three ways to download the source code of OrthoFinder locally into a directory named OrthoFinder.

# Download via git 
git clone https://github.com/OrthoFinder/OrthoFinder.git
# or download the orthofinder-linux-intel-3.1.0.tar.gz and unzip it into OrthoFinder if you are on a Linux Intel machine
mkdir OrthoFinder && \
  wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.0/orthofinder-linux-intel-3.1.0.tar.gz | \
  tar -xz --strip-components=1 -C OrthoFinder

Next, you can run the following commands to install OrthoFinder inside the of3_env virtural environment.

cd OrthoFinder
python3 -m venv of3_env # Create an virtural environment named of3_env
. of3_env/bin/activate # Activate of3_env
pip install .

Whether you’ve installed OrthoFinder directly from GitHub or downloaded and set it up locally, the OrthoFinder package will only be available within the of3_env virtual environment. This avoids potential conflicts with Python dependencies.

To deactivate the virtual environment when you are finished, run:

deactivate

To activate the virtual environment you have created, run:

. of3_env/bin/activate

Test your installation

Once you have installed OrthoFinder, you can print the help information and version, and test it on the example data.

orthofinder --help # Print out help informatioin
orthofinder --version # Check the version
orthofinder -f ExampleData # Test OrthoFinder on an example dataset

Uninstalling

To uninstall on conda:

conda deactivate
conda remove -n of3_env --all

To remove the virtual environment where OrthoFinder is installed:

deactivate
cd ..
rm -rf OrthoFinder