📦 orthofinder-linux-intel-3.1.0.tar.gz
📦 orthofinder-linux-arm-3.1.0.tar.gz
📦 orthofinder-macos-arm-3.1.0.tar.gz
📦 orthofinder-macos-intel-3.1.0.tar.gz
📦 orthofinder-macos-universal-3.1.0.tar.gz

🧬 Input

  • Protein or codon MSA (FASTA format)
  • Defined outgroup species or clade
  • (Optional) Species tree in Newick format — used to constrain phylogenetic inference if provided

📤 Output

  • *.OrthoFinder.tsv — list of OrthoFinderrent amino acid substitutions inferred from the tree
  • .OrthoFinder/ — directory containing intermediate files:
    • Model selection output
    • Inferred phylogenetic tree
    • Ancestral state reconstructions
    • Site substitution matrices

⚙️ Dependencies

  • OrthoFinder v3.1.0 includes the IQ-TREE2 binary (bundled in OrthoFinder/bin/) and uses it for:
    • Phylogenetic tree inference
    • Ancestral sequence reconstruction
    • Simulation of alignments for null models

No external installation of IQ-TREE2 is required.

⬇️ Dowload

  • orthofinder-linux-intel-3.1.0.tar.gz 
    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
  • orthofinder-linux-arm-3.1.0.tar.gz 
    mkdir OrthoFinder && \
  wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.0/orthofinder-linux-arm-3.1.0.tar.gz | \
  tar -xz --strip-components=1 -C OrthoFinder
  • orthofinder-macos-arm-3.1.0.tar.gz 
    mkdir OrthoFinder && \
  wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.0/orthofinder-macos-arm-3.1.0.tar.gz | \
  tar -xz --strip-components=1 -C OrthoFinder
  • orthofinder-macos-intel-3.1.0.tar.gz 
    mkdir OrthoFinder && \
  wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.0/orthofinder-macos-intel-3.1.0.tar.gz | \
  tar -xz --strip-components=1 -C OrthoFinder
  • orthofinder-macos-universal-3.1.0.tar.gz 
    mkdir OrthoFinder && \
  wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.0/OrthoFinder-iqtree2-macos-universal-3.1.0.tar.gz | \
  tar -xz --strip-components=1 -C OrthoFinder

📦 Install

  • Linux and MacOS 
      cd OrthoFinder
  python3 -m venv of3_env 
  . of3_env/bin/activate
  pip install .
  OrthoFinder --version
  OrthoFinder -f ExampleData/example_alignments.aln -st AA --outgroups ExampleData/example_alignments.outgroups.txt

    To deactivate the virtual environment, run

      deactivate

    Having deactivated the virtual environment, to remove OrthoFinder, please run

      cd ..
  rm -rf OrthoFinder