Phage and virus biology · Software
taxmyPHAGE
Classifies complete dsDNA bacteriophage genomes to genus and species following official ICTV guidelines.
What taxmyPHAGE is
taxmyPHAGE is a computational tool developed by Andrew Millard, Thomas Sicheritz-Ponten and Remi Denise to classify bacteriophage genomes according to official International Committee on Taxonomy of Viruses (ICTV) criteria. Phage taxonomy evolves rapidly, and determining whether a newly sequenced isolate belongs to an established genus or species, or represents a novel taxon, typically requires laborious manual comparison against classified viral genomes.
The software automates taxonomic assignment at the genus and species levels for double-stranded DNA (dsDNA) phages. It compares query sequences against reference bacteriophages catalogued in the ICTV Virus Metadata Resource (VMR), allowing researchers to rapidly determine the taxonomy of newly sequenced phage isolates and identify potential novel genera without manually curating comparison datasets.
taxmyPHAGE operates via a command-line interface or an online web version, comparing query sequences against curated databases of ICTV-classified phage genomes such as those distributed via the INPHARED project.
How it works
The pipeline takes individual complete phage genomes in FASTA format and performs an initial search using Mash to identify close relatives from a precomputed sketch database of ICTV-classified dsDNA phages. By default, a Mash distance cutoff of 0.2 is applied to select candidate related reference genomes.
Once close relatives are identified, the tool retrieves reference sequences and performs an intergenomic comparison using BLASTn. It calculates pairwise similarities using the same formula implemented by VIRIDIC (Virus Intergenomic Distance Calculator). Using current ICTV percentage identity thresholds for genus-level and species-level delineation, taxmyPHAGE clusters the query alongside reference genomes and interprets the genomic similarity to determine whether the isolate falls into an existing genus or species, represents a new species within a known genus, or constitutes an entirely novel genus.
Key facts
- Authors
- Andrew Millard, Thomas Sicheritz-Ponten and Remi Denise
- Target organisms
- Double-stranded DNA (dsDNA) bacteriophages
- Taxonomic levels
- Genus and species
- Reference databases
- ICTV Virus Metadata Resource (VMR) and INPHARED-derived ICTV bacteriophage genomes
- Input formats
- FASTA, FNA, FSA, FA (uncompressed or gzip-compressed)
- Output formats
- TSV, TXT, CSV, PDF, PNG, SVG
- External dependencies
- MASH (>= 2.3) and NCBI BLAST+ (>= 2.14.0)
What you can use it for
- Bacteriophage genus and species assignment
- Assign taxonomy to newly sequenced complete dsDNA bacteriophages based on up-to-date ICTV taxonomic boundaries.
- Novel genus identification
- Establish whether an unclassified phage isolate falls outside existing ICTV-recognised genera and represents a candidate new genus.
- Pairwise intergenomic distance analysis
- Compute VIRIDIC-like genomic similarity matrices and generate similarity heatmaps between input phages and reference genomes using the similarity module.
Run it here
Ask the research agent and it runs taxmyPHAGE as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
Strengths and limits
Good at
- Automates taxonomy assignment using officially recognised ICTV demarcation thresholds without requiring full manual VIRIDIC runs.
- Efficiently filters large reference databases by employing Mash sketching before conducting detailed nucleotide BLAST alignments.
- Generates publication-ready figures, including similarity heatmaps in PDF, PNG and SVG formats.
- Scales across modern laptops and multi-core servers, handling multiple input genomes in batch mode.
Watch out for
- Not intended for metagenomic assemblies, fragmented contigs, or eukaryotic viruses.
- Cannot reliably classify RNA phages or single-stranded DNA (ssDNA) phages.
- Does not assign phages into newly defined families or compare queries against unclassified GenBank phage sequences.
- Requires substantial compute time when comparing against large genera containing dozens of classified species.
Questions
Can I run taxmyPHAGE online without installing it?
Ask the research agent and it runs taxmyPHAGE as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
What licence is taxmyPHAGE under?
MIT. The terms are published at https://github.com/amillard/tax_myPHAGE.
What inputs does taxmyPHAGE accept?
It accepts single complete phage genome sequences or directories of genomes in FASTA format (extensions .fasta, .fna, .fsa, or .fa), which may be gzip-compressed.
Can taxmyPHAGE classify metagenomic viral contigs?
No. The pipeline is designed specifically for individual, complete dsDNA bacteriophage isolate genomes and cannot process metagenomic samples.
Does taxmyPHAGE directly run VIRIDIC?
No. It runs an independent VIRIDIC-like analysis using the exact same genomic comparison formula implemented in VIRIDIC to calculate pairwise intergenomic similarity.
What should I do if my phage fails to match an existing genus?
Increasing the Mash distance parameter (-d or --distance) from the default 0.2 to 0.3 can help retrieve distant relatives and generate output files confirming that the isolate falls outside current genera.
Written from taxmyPHAGE's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.