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Taxonomy and classification

Most giant viruses recovered from metagenomes have no named relative. Placing one in the tree of life means asking which known reference sits closest, marker by marker, and trusting that answer only as far as the references reach. GVClass treats classification as a phylogenetic placement problem and keeps the call deliberately conservative.

From marker trees to a lineage

Classification rests on the per-marker trees the pipeline builds during a run (see How it works). Every conserved marker that a query carries gets its own single-gene tree, aligned against the top reference hits for that marker. From each tree GVClass reads the nearest reference neighbour of the query and records that neighbour's lineage. One marker, one vote.

The votes are tallied rank by rank. For each level from domain down to species, the lineage that the most markers point to becomes the call, and the per-taxon vote counts are kept beside it. The concatenated result lands in taxonomy_majority, while the individual rank columns (species through domain) carry the winning taxon with its count. avgdist records the mean tree distance from the query to those nearest references, a first read on how far the query sits from anything known.

For the bundled example genome PkV-RF01, the markers agree on d_NCLDV;p_Nucleocytoviricota;c_Megaviricetes;o_Imitervirales;f_IM_19;g_g1787;s_singleton. The lineage resolves cleanly to family IM_19, then narrows to a single reference genus (g1787) and a species placeholder (s_singleton).

Note

Genus and species identifiers like g1787 and s_singleton are reference-derived labels from the GVClass database, not formal binomial names. s_singleton means the query placed on its own with no close species-level reference.

Why confidence varies

taxonomy_confidence summarises how well the vote held up. A call is high only when every emitted rank cleared its distinct-marker threshold, meaning enough independent markers, not duplicate copies of one, agreed at that level. When a rank is emitted on too few distinct markers, the value drops to low_support. reduced_fastmode appears when fast mode (the default) skipped the order-level marker panel, so order resolution rests on the core set alone; build trees for all markers with -e/--extended to lift that flag. no_support marks a query whose markers could not agree on a lineage at all. PkV-RF01 reports high. Read this column together with the quality metrics, since duplicated markers inflate raw vote counts without adding independent evidence.

Where the calls are trustworthy

The deep ranks are the dependable ones. Domain, phylum, class, order, and family draw on conserved markers whose reference trees are well sampled, so the majority vote at those levels is stable and reproducible. Genus and species behave differently. The pipeline reports the name of whatever genome sat closest in the marker trees, a nearest-reference label rather than an ICTV assignment. A genus or species call carries weight only when the query is close to a reference: a low avgdist and a real species match instead of an s_singleton placeholder. For a novel GVMAG, read the family and treat the genus and species as a pointer to the nearest known thing.

For genome-level confirmation at the tips, the opt-in species tree concatenates a domain's core markers into one supermatrix and reports an independent nearest-reference placement in the four species_tree_* columns (see also the how-to guide).

Registered domains

GVClass classifies into three registered viral domains, each with its own marker panel and reference set (full panel sizes are in the markers reference):

  • NCLDV (Nucleocytoviricota), the nucleocytoplasmic large DNA viruses, scored on the GVOG4 and GVOG8 core panels.
  • PPV (Preplasmiviricota), the unified domain holding virophages and Polinton-like viruses, scored on the virophage core (MCP, Penton, ATPase, Protease) plus the A32/plv PPV-membership marker.
  • MIRUS (Mirusviricota), scored on the four-marker Mirus core (MCP, ATPase, Portal, Triplex).

A genome that falls in none of these is left unclassified rather than forced into a domain.

Capsid typing

Two columns describe the major capsid protein (MCP) signal. capsid_group is a label:count tally across the MCP panels, for example Nucleocytoviricota:4,Gossevirus:1, spanning the Nucleocytoviricota and Mirusviricota phyla and the Bellas & Sommaruga capsid groups.

Within PPV, plv tells the two members apart. It counts A32 ATPase proteins (the PLV_PC_054 marker) that place with PPV references in the marker tree. A32 is shared with NCLDV, so only copies that branch inside PPV are counted, which keeps plv at 0 for an ordinary NCLDV genome. Among PPV members, virophages and Polinton-like viruses both carry the virophage MCP markers (vp_completeness, vp_mcp), and a higher plv count leans the call toward a Polinton-like virus. The count is graded, not a yes/no flag.

What changed in v2.0

Earlier versions split these capsid-related viruses into two separate labels, PLV and VP. v2.0 unifies them under PPV as one monophyletic Preplasmiviricota domain, backed by a re-curated PPV reference set. The ICTV-2025 rename of Maveriviricetes to Virophaviricetes is applied throughout the database, so virophage class names follow current nomenclature.

Reading the result conservatively

Together these choices keep the output honest about its own reach. GVClass reports the deepest lineage the markers support, records how much support that was, and labels the tips as nearest references rather than formal species. Read the family with confidence, read the genus and species as the closest known neighbour, and check taxonomy_confidence and avgdist before trusting either. Every column named here is defined in the output reference.