orthofinder/recur repository overview

⁠🧬 Introduction

This image runs RECUR, a phylogenetic tool that detects recurrent amino acid (or codon) substitutions across a tree inferred from a multiple sequence alignment. The recurrence analysis implemented by RECUR utilises IQ-TREE3 (v3.1.1) phylogenomic software package to infer a phylogeny, reconstruct ancestral node sequences, and generate simulated alignments.

⁠📥 Input

• Protein or codon MSA in FASTA format
• Defined outgroup species or clade
• Species tree (Optional)

⁠📤 Output

• *.recur.tsv: List of recurrent substitutions
• Tree inference, ancestral state reconstructions, and substitution matrices (*.recur/ directory)

⁠🚀 RECUR v1.1.0

This release introduces multiple-testing correction and improved scalability for large Monte Carlo analyses.

⁠✨ New Features

• Multiple-testing correction
  (Bonferroni, Holm, BH, two-stage BH, BKY/FDR)
• Automatic multistage Monte Carlo computation
• Backend upgraded to IQ-TREE3

⁠⚡ Improvements

• Improved scalability and disk safety
• Enhanced performance for large datasets
• Updated Docker environment

⁠🐳 Docker

Pull the latest version:

docker pull orthofinder/recur:v1.1.0

⁠🚀 Usage:

⁠▶️ Run the ExampleData

docker run -it --rm \
    -v "$(pwd)/ExampleData:/usr/src/recur/ExampleData" \
    -e LOCAL_UID=$(id -u) -e LOCAL_GID=$(id -g) \
    orthofinder/recur:v1.1.0 \
    -f ExampleData/example_alignments.aln \
    -st AA \
    --outgroups ExampleData/example_alignments.outgroups.txt \
    -te ExampleData/example_alignments.tree.txt

⁠▶️ Run your own data

1. Create your Data directory, for instance MyData.
2. Replace the corresponding alignment file, outgroups file, and tree file paths in the following command, then hit enter.

docker run -it --rm \
    -v $(pwd)/MyData:/usr/src/recur/MyData \
    -e LOCAL_UID=$(id -u) -e LOCAL_GID=$(id -g) \
    orthofinder/recur:v1.1.0 \
    -f MyData/my_alignments.aln \
    -st AA \
    --outgroups MyData/my_alignments.outgroups.txt \
    -te MyData/my_alignments.tree.txt