nf-core pipeline · evolutionary-models, msa, natural-selection
nf-core/genephylomodeler
A bioinformatics pipeline that fits evolutionary models and detects natural selection in protein-coding gene alignments.
What nf-core/genephylomodeler is
nf-core/genephylomodeler is a bioinformatics pipeline designed to detect natural selection and fit evolutionary models from multiple sequence alignments of protein-coding genes. It automates hypothesis testing across sequence data by executing specialised evolutionary analysis tools across user-specified gene alignments and phylogenetic trees. The pipeline was originally written by Nina Xiong, with development assistance from Areeba Rahu and Nuha Kadak.
Understanding molecular evolution requires identifying whether genetic sequences are subject to neutral evolution, positive selection, purifying selection, or relaxed constraints. nf-core/genephylomodeler streamlines this process by executing codon-based comparative methods from established suites including HyPhy and PAML, outputting statistical results in structured text and JSON formats.
What the pipeline does
The workflow accepts a samplesheet in CSV format specifying gene names, paths to multiple sequence alignments, phylogenetic tree files, and the requested analytical suite and tool. For analyses requiring PAML, a path to a control file is also supplied. The pipeline coordinates the execution of each requested method across the designated input alignments and trees.
Depending on the configuration in the samplesheet, the pipeline carries out selection screening, recombination detection, or model fitting using tools from HyPhy or PAML CODEML. The results of the analyses are compiled and exported as text and JSON files.
Key facts
- Pipeline engine
- Nextflow
- Original developer
- Nina Xiong
- Primary input
- CSV samplesheet with alignment and phylogenetic tree paths
- Output formats
- JSON, text
- Integrated software suites
- HyPhy, PAML
- Supported HyPhy tools
- aBSREL, BGM, BUSTED, FADE, FEL, FUBAR, GARD, MEME, RELAX, SLAC
- Supported PAML tools
- CODEML
What you can use it for
- Episodic and branch-specific selection detection
- Identify lineage-specific positive selection or gene-wide episodic diversifying selection using HyPhy methods such as aBSREL and BUSTED.
- Site-level selection analysis
- Detect individual codon sites evolving under positive diversifying or purifying selection using HyPhy tools including FEL, FUBAR, MEME, and SLAC.
- Selection intensity testing
- Test whether selection pressure has been relaxed or intensified across specified branches of a phylogenetic tree using HyPhy RELAX.
- Recombination screening
- Screen alignments for recombination breakpoints prior to phylogenetic inference using HyPhy GARD.
- Maximum likelihood codon substitution modelling
- Fit evolutionary codon substitution models and estimate substitution rates across gene trees using PAML CODEML.
Run it here
The research agent runs nf-core/genephylomodeler with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Incorporates ten distinct evolutionary hypothesis testing and selection detection methods from the HyPhy suite alongside PAML CODEML.
- Enables simultaneous execution of varied evolutionary methods across different genes within a single unified samplesheet.
- Outputs analysis findings in structured JSON and text formats suitable for downstream parsing and automated analysis.
Watch out for
- Running the workflow with Docker on macOS fails unless the arm64 profile is specified because HyPhy's Docker image is built for linux/amd64.
- Pipeline parameters cannot be supplied through custom configuration files using the Nextflow -c flag and must be passed via the command line or a parameters file.
Questions
Can I run nf-core/genephylomodeler without my own cluster?
The research agent runs nf-core/genephylomodeler with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/genephylomodeler under?
MIT, like every nf-core pipeline.
What inputs does the pipeline require?
The pipeline requires a CSV samplesheet defining the gene name, alignment file path, phylogenetic tree file path, suite name, tool name, and any required control file such as for CODEML.
Which HyPhy methods are supported?
The supported HyPhy methods are aBSREL, BGM, BUSTED, FADE, FEL, FUBAR, GARD, MEME, RELAX, and SLAC.
How are PAML CODEML runs configured?
PAML analyses are selected by specifying the paml suite and codeml tool in the samplesheet, accompanied by a path to a CODEML control file.
Why does the pipeline need a special profile when running Docker on macOS?
HyPhy's Docker container image is linux/amd64, so users on macOS must specify -profile docker,arm64 to enable proper execution.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/genephylomodeler's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.