This repository provides a reproducible pipeline for phylogenetic analysis using Nextflow, BLASTP, CD-HIT, MAFFT, trimAl, and IQ-TREE. The workflow supports automated BLAST search, clustering, alignment, trimming, and tree inference for protein. The pipeline is highly configurable, allowing users to control each step with parameters.

• Automated environment setup with Conda
• BLASTP search against a user-specified protein database
• Limit the number of BLAST hits retrieved (parameterized)
• Sequence clustering with CD-HIT (optional)
• Combine original and clustered sequences (optional)
• Multiple sequence alignment using MAFFT
• Alignment trimming with trimAl
• Phylogenetic tree inference using IQ-TREE (optional)
• Highly configurable workflow via Nextflow parameters
• Organized output directories for results

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

Clone the repository:

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

Set up the Conda environment:

source env/setup.sh

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

Prepare your input files:

• Place your FASTA files in inputs/

Run the pipeline with default settings:

nextflow run main.nf --blast_db /path/to/your/blastdb

• --blast_num_seq 500 : Number of BLAST hits to retrieve per query (default: 500)
• --cd_hit true : Enable CD-HIT clustering (default: false)
• --cd_hit_ident 0.9 : CD-HIT identity threshold (default: 0.9)
• --combine true : Combine original and clustered sequences before alignment (default: false)
• --phylogeny true : Run alignment, trimming, and tree inference (default: false)

Example with clustering and phylogeny:

nextflow run main.nf --blast_db /path/to/your/blastdb --cd_hit true --cd_hit_ident 0.95 --combine true --phylogeny true

Results are saved in the results/ directory:

• results/blast/ for BLAST outputs and extracted FASTA
• results/cdhit/ for clustered and/or combined FASTA files
• results/mafft/ for alignments
• results/trimal/ for trimmed alignments
• results/iqtree/ for phylogenetic trees

Conda environment not activated: Always use source env/setup.sh to ensure the environment is activated in your current shell.

Missing dependencies: Re-run the setup script or check env/env.yaml.

No results produced: Check that your input files are in the correct inputs/ directory and that the BLAST database path is correct.

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

If you use this pipeline, please cite BLAST, CD-HIT, MAFFT, trimAl, IQ-TREE, and Nextflow.

Alejandro Jiménez-González