Table 1. Examples of methodologies used for virus classification at different taxonomic ranks*.
| Method | Principle | Rank range | Ref |
|---|---|---|---|
| DEmARC | Analysis of distributions of pairwise evolutionary distances between nucleotide or amino acid sequences | Suborder, Family, Subfamily, Genus, Subgenus, Species | [38] |
| GRAViTy | Virus relationships from composite Jaccard distances between HMM profiles and genome organizational models | Order, Family, (Genus) | [46] |
| HSF | Identification of structural equivalence and calculation of structural distances for structure-based phylogenetics | Realm, Kingdom, Phylum, Class, Order, Family, Genus | [58,68] |
| PASC | Analysis of pairwise nucleotide sequence distance distributions | Genus, Species | [37] |
| PhageClouds | Graph database of phage genomic sequences and intergenomic distances | Subfamily, Genus, Species | [69] |
| SDT | Pairwise nucleotide sequence alignment and identity calculation | Species | [70] |
| vConTACT2 | Whole-genome gene sharing profiles integrating hierarchical clustering and confidence scores | Order, Family, Subfamily, Genus | [44,45] |
| VICTOR | Phylogenomic method optimized to ICTV classification that reports both sequence identity- and gene content-based phylogenies along with a suggested classification; works with either nucleotide or amino acid datasets | Family, Subfamily, Genus, Species | [42] |
| ViPTree | Virus relationships from genomic distances based translated nucleotide scores using tBLASTx | Family, Subfamily, Genus | [49] |
| VirClust | Hierarchical clustering based on core protein analysis | Order, Family, Subfamily | [71] |
| VIRIDIC | Calculates intergenomic similarities between pairs of viral genomes based on BLASTN alignments | Family, Genus, Species | [39] |
*Discussions of tools dedicated to general reconstruction of phylogeny based on multiple sequence alignments are beyond the scope of this paper (for more information about this subject, see [72,73]). A more extensive list of virus bioinformatics tools including tools for virus taxonomy can be found at https://evirusbioinfc.notion.site/evirusbioinfc/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947.