Ancestral Sequence Reconstruction Pipeline (asr-nf)

This repository provides a reproducible pipeline for ancestral sequence reconstruction using Nextflow and IQ-TREE. The workflow supports iTOL visualization, taxonomy annotation, and extraction of ancestral FASTA sequences for selected nodes.

Features

• Automated environment setup with Conda
• Ancestral state reconstruction using IQ-TREE
• iTOL-compatible outputs for visualization
• Flexible FASTA extraction for all or selected ancestral nodes
• Taxonomy annotation for visualization (optional)

Requirements

• Miniconda/Anaconda
• Nextflow (installed via Conda environment)

Installation

1. Clone the repository:

   git clone https://github.com/alejimgon/asr-nf.git
   cd asr-nf

2. Set up the Conda environment:

   source scripts/setup.sh

   This will create and activate the asr-nf environment with all dependencies.

Usage

1. Prepare your input files:

   • Place your alignment files in data/alignments/
   • Place your tree files in data/phylogenetic_trees/
   • Edit data/input_table.txt with your analysis parameters (see below).

2. Run the pipeline:

   nextflow run main.nf

3. Optional parameters:

   • Fetch taxonomy and generate iTOL labels:

     nextflow run main.nf --tax true --email your_email@example.com

   • Extract FASTA for all or selected nodes:

     nextflow run main.nf --extract_fasta true
     nextflow run main.nf --extract_fasta true --fasta_nodes Node13,Node25
     nextflow run main.nf --extract_fasta true --fasta_nodes "Nodes13|Nodes25"
     nextflow run main.nf --extract_fasta true --fasta_nodes my_nodes.txt
     nextflow run main.nf --extract_fasta true --fasta_missing X

Input Table Format

data/input_table.txt should be a tab-delimited file with the following columns (no header):

alignment_file   model   position   aa   asr_min

Example:

example.aln   JTT+G   42   K   0.7

Output

• Results are saved in the outputs/ directory.
• iTOL files and extracted FASTA sequences are organized by analysis.

Troubleshooting

• Conda environment not activated:
  Always use source scripts/setup.sh to ensure the environment is activated in your current shell.
• Missing dependencies:
  Re-run the setup script or check env/env.yaml.

License

This project is for non-commercial use.
See LICENSE for details.

Citation

If you use this pipeline, please cite IQ-TREE and Nextflow.

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Developed

Developed by Alejandro Jiménez-González