RECUR-v1.0.0

📦 recur-iqtree2-linux-intel-1.0.0.tar.gz

📦 recur-iqtree2-linux-arm-1.0.0.tar.gz

📦 recur-iqtree2-macos-arm-1.0.0.tar.gz

📦 recur-iqtree2-macos-intel-1.0.0.tar.gz

📦 recur-iqtree2-macos-universal-1.0.0.tar.gz

📦 recur-iqtree2-windows-1.0.0.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

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📤 Output

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

---

⚙️ Dependencies

• RECUR v1.0.0 includes the IQ-TREE2 binary (bundled in recur/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

• recur-iqtree2-linux-intel-1.0.0.tar.gz

  mkdir RECUR && \
    wget -qO- https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-linux-intel-1.0.0.tar.gz | \
    tar -xz --strip-components=1 -C RECUR
  

• recur-iqtree2-linux-arm-1.0.0.tar.gz

  mkdir RECUR && \
    wget -qO- https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-linux-arm-1.0.0.tar.gz | \
    tar -xz --strip-components=1 -C RECUR
  

• recur-iqtree2-macos-arm-1.0.0.tar.gz

  mkdir RECUR && \
    wget -qO- https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-macos-arm-1.0.0.tar.gz | \
    tar -xz --strip-components=1 -C RECUR
  

• recur-iqtree2-macos-intel-1.0.0.tar.gz

  mkdir RECUR && \
    wget -qO- https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-macos-intel-1.0.0.tar.gz | \
    tar -xz --strip-components=1 -C RECUR
  

• recur-iqtree2-macos-universal-1.0.0.tar.gz

  mkdir RECUR && \
    wget -qO- https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-macos-universal-1.0.0.tar.gz | \
    tar -xz --strip-components=1 -C RECUR
  

• recur-iqtree2-windows-1.0.0.tar.gz

  • Command Prompt

    mkdir RECUR && \
        curl -L -o recur.tar.gz https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-windows-1.0.0.tar.gz && \
        tar -xzf recur.tar.gz -C RECUR --strip-components=1 && \
        del recur.tar.gz
    

  • PowerShell

    New-Item -ItemType Directory -Force -Path '\RECUR'
    Invoke-WebRequest -Uri 'https://github.com/OrthoFinder/RECUR/releases/download/v1.0.0/recur-iqtree2-windows-1.0.0.tar.gz' -OutFile 'recur.tar.gz'
    tar -xzf 'recur.tar.gz' -C 'RECUR' --strip-components=1
    Remove-Item 'recur.tar.gz'
    

📦 Install

• Linux and MacOS

    cd RECUR
    python3 -m venv recur_env 
    . recur_env/bin/activate
    pip install .
    recur --version
    recur -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 RECUR, please run

    cd ..
    rm -rf RECUR
  

• Windows

    cd RECUR
    python -m venv recur_env
    .\recur_env\Scripts\activate.bat
    pip install .
    recur --version
    recur -f ExampleData/example_alignments.aln -st AA --outgroups ExampleData/example_alignments.outgroups.txt 
  

  To deactivate the virtual environment, run

    .\recur_env\Scripts\deactivate.bat
  

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

  • Command Prompt

      cd ..
      rmdir /s /q RECUR
    

  • PowerShell

      cd ..
      Remove-Item -Recurse -Force .\RECUR