Viruses and CRISPR · What you can do here
Classify a phage to ICTV genus and species
Classify bacteriophage genomes to ICTV genus and species using taxmyPHAGE and the INPHARED database, applying the official 70% and 95% nucleotide identity thresholds.
What this involves
Taxonomic classification of bacteriophages follows explicit nucleotide identity boundaries defined by the International Committee on Taxonomy of Viruses (ICTV). The ICTV standards assign genomes sharing at least 95% nucleotide identity to the same species, and genomes sharing at least 70% nucleotide identity to the same genus. Running classification with taxmyPHAGE tests your sequence directly against these criteria using INPHARED, the curated reference database maintained by the Millard lab.
Bacteriophage analysis requires establishing sequence quality and provenance before drawing taxonomic conclusions. If your input derives from an uncharacterised assembly or integrated provirus, you should first identify viral boundaries with geNomad and assess genome completeness with CheckV. When evaluating proviruses, classification must run on the trimmed proviral sequence rather than the surrounding bacterial contig.
If your genome falls below the 70% genus-level identity threshold, it represents a candidate new genus rather than an ambiguous failure. The platform's research agent runs taxmyPHAGE in a persistent workspace on a dedicated machine, allowing you to trace reference matches without local installation or manual database configuration.
How it goes
- 1Prepare and verify sequence inputProvide a nucleotide accession such as NC_001416.1, a FASTA file path in /work/uploads/, or a URL. If you have an assembly accession such as a GCF_ identifier, fetch the genomic FASTA first.
- 2Assess completeness and trim provirusesRun CheckV to establish the MIUViG quality tier and ensure genome completeness. If analysing integrated phage sequences, isolate CheckV's trimmed proviruses to avoid host contig contamination.
- 3Classify taxonomy with taxmyPHAGEExecute taxmyPHAGE against the INPHARED database to calculate pairwise nucleotide identities and assign ICTV species at the 95% threshold and ICTV genus at the 70% threshold.
- 4Evaluate candidate novel taxaInspect borderline or non-matching results; any phage sequence failing to match an existing group at the 70% threshold is identified as a candidate new genus.
Start it here
Ask in plain language. The agent works on a Linux machine of its own — it installs and runs what the job needs, keeps every file, and reads the results back with the numbers explained. Nothing to set up, and a long run continues after you close the page.
What to watch for
- A genome matching no ICTV genus is a candidate new genus, which is a significant finding rather than an unclassified error.
- CheckV's trimmed proviruses, not the raw host contigs, are what should be supplied for downstream annotation and classification.
- An assembly accession starting with GCF_ is not a sequence, so the genomic FASTA must be retrieved before running taxmyPHAGE.
- Completeness is relative to reference sets, meaning a novel phage lacking close relatives may score low simply for want of a comparator.
What it runs
Questions
Do I need to install anything to classify a phage to ictv genus and species?
No. The research agent does this work on a Linux machine of its own — it runs taxmyPHAGE, Pharokka there, keeps the files, and reads the results back to you. Long runs continue if you close the page.
What nucleotide identity thresholds define an ICTV genus and species?
Under ICTV rules applied by taxmyPHAGE, genomes sharing at least 95% nucleotide identity belong to the same species, while those sharing at least 70% nucleotide identity belong to the same genus.
What reference database does taxmyPHAGE use?
taxmyPHAGE classifies genomes using INPHARED, the curated phage genome dataset maintained by the Millard lab.
What happens if my phage sequence does not match any known genus?
A genome that falls below the 70% identity threshold to known ICTV genera is considered a candidate new genus.
Can I supply an NCBI assembly accession directly to the tool?
No, an assembly accession such as GCF_ is not a sequence; you must fetch the genomic FASTA file first before running classification.
Written from the method the research agent follows for this work and the documentation of the tools listed above. Statements citing a figure that does not appear there are removed before publication. Corollary is a non-commercial research demonstration; results are not for clinical use.