nf-core pipeline · evolution, evolutionary-tree, phylogenetic-placement
nf-core/phyloplace
A Nextflow pipeline for phylogenetic placement and taxonomic classification of query sequences using EPA-NG and GAPPA.
What nf-core/phyloplace is
nf-core/phyloplace is a bioinformatics analysis pipeline designed for phylogenetic placement, a method that positions query sequences directly onto an existing reference evolutionary tree rather than inferring a new tree from scratch. The pipeline was originally written by Daniel Lundin and is maintained within the nf-core framework using Nextflow DSL2 with process containerisation.
The pipeline resolves the challenge of integrating novel or uncharacterised sequence data into established phylogenetic frameworks. It facilitates rapid evolutionary placement, tree grafting, and subsequent taxonomic sequence classification.
What the pipeline does
The workflow can optionally start by querying an input FASTA file with a collection of HMMER profiles, identifying the highest-scoring hits for each profile to use as query sequences. Next, query sequences are aligned to a reference alignment using HMMER, Clustal Omega (clustalo), or MAFFT.
Following alignment, EPA-NG places the query sequences onto a user-supplied reference phylogeny. GAPPA is then used to graft the placed sequences onto the tree. If taxonomic annotations are provided separately or can be parsed from the reference sequence FASTA headers, GAPPA also determines the taxonomic classification for each query sequence.
Key facts
- Original author
- Daniel Lundin
- Latest release
- 2.1.0
- Workflow framework
- Nextflow DSL2
- Placement engine
- EPA-NG
- Tree grafting and classification
- GAPPA
- Supported aligners
- HMMER, Clustal Omega (clustalo), MAFFT
- Input formats
- FASTA, HMM profiles, phylogenetic tree files, taxonomy files (plain text or gzipped), CSV
What you can use it for
- Phylogenetic tree placement
- Place query sequences onto an existing reference tree using EPA-NG without re-estimating the entire phylogeny.
- Taxonomic sequence classification
- Classify query sequences based on reference phylogeny and reference taxonomy data using GAPPA.
- Profile-based sequence extraction and placement
- Search a sequence file against HMMER profiles to select the best hits and automatically feed them into downstream alignment and placement steps.
Run it here
The research agent runs nf-core/phyloplace 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
- Supports multiple sequence alignment engines including HMMER, Clustal Omega, and MAFFT.
- Performs both phylogenetic placement and phylogenetic grafting into a single reference tree.
- Directly derives query classifications from reference annotations using GAPPA.
- Accepts gzipped sequence, profile, tree, and taxonomy input files.
Watch out for
- Query classification depends on having reference sequence taxonomy supplied either in an explicit classification file or within reference FASTA headers.
- Pipeline execution parameters cannot be passed via custom Nextflow configuration files and must be supplied by command line or parameter files.
Questions
Can I run nf-core/phyloplace without my own cluster?
The research agent runs nf-core/phyloplace 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/phyloplace under?
MIT, like every nf-core pipeline.
Which tools can be used for sequence alignment?
Query sequences can be aligned to the reference alignment using HMMER, Clustal Omega (clustalo), or MAFFT.
Can input files be compressed?
Yes, input sequence, profile, tree, and taxonomy files may all be supplied in gzipped format.
How are query sequences classified?
Query sequences are classified by GAPPA using taxonomy information provided either in an explicit classification input or directly in the FASTA headers of the reference sequence file.
What is the purpose of the optional initial search step?
The optional search step scans a FASTA file using HMMER profile models and extracts the best hits to pass into the subsequent alignment and placement stages.
How to cite it
10.5281/zenodo.7643941
Written from nf-core/phyloplace's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.