Phylogeny (AAI and ANI)

ANI calculator

ANI (Average Nucleotide Identity) calculator - estimates the average nucleotide identity using both best hits (one-way ANI) and reciprocal best hits (two-way ANI) between two genomic datasets. Typically, the ANI values between genomes of the same species are above 95% (e.g., Escherichia coli). Values below 75% are not to be trusted, and AAI should be used instead. This tool supports both complete and draft genomes (multi-fasta).
(Reference: Goris J et al. 2007. Int J Syst Evol Microbiol. 57(Pt 1): 81-91).
Also see ANI calculator and FastANI which is part of the KBase suite of programs (requires registration).

Average Nucleotide Identity

Average Nucleotide Identity (ANI) calculator - their ANI Calculator uses the OrthoANIu algorithm, an improved iteration of the original OrthoANI algorithm, which uses USEARCH instead of BLAST
(Reference: Yoon, S. H. et al. (2017). Antonie van Leeuwenhoek. 110:1281-1286).

VIRIDIC

VIRIDIC (Virus Intergenomic Distance Calculator; C. Moraru, Institute for Chemistry and Biology of the Marine Environment, Germany) - the first level of bacteriophage classification by ICTV involves computing the overall DNA sequence identity between two viruses. This new tool computes pairwise intergenomic distances/similarities amongst phage genomes. To run it, upload a single fasta file with all phage genomes of interest, create a project and press run. Save the project ID that will be displayed when the project is created. You will need it to access the data if the calculations take a long time
(Reference: Moraru C et al. 2020. Viruses. 12(11): 1268).

GGDC

GGDC (Genome-To-Genome Distance Calculator) - provides methods for inferring whole-genome distances which are well able to mimic DNA-DNA hybridization (DDH). Values calculated with GGDC yield a somewhat better correlation with wet-lab DDH values than alternative approaches such as "ANI". These distance functions can also cope with heavily reduced genomes and repetitive sequence regions. Some of them are also very robust against missing fractions of genomic information (due to incomplete genome sequencing). Thus, this web service can be used for genome-based species delineation.
(Reference: Meier-Kolthoff JP et al. 2013. BMC Bioinformatics 14: 60).

POGO-DB

POGO-DB - Based on computationally intensive whole-genome BLASTs, POGO-DB provides several metrics on pairwise genome: (a) Average Amino Acid Identity of all bi-directional best blast hits that covered at least 70% of the sequence and had 30% sequence identity; (b) Genomic Fluidity that estimates the similarity in gene content between two genomes; (c) Number of orthologs shared between two genomes (as defined by two criteria); (d) Pairwise identity of the most similar 16S rRNA genes; (e) Pairwise identity of 73 additional globally-conserved marker genes (which were determined by us to exist in at least 90% of all the genomes).
(Reference: Lan Y et al. 2014. Nucl. Acids Res. 42(D1): D625-D632).

VICTOR

VICTOR (Virus Classification and Tree Building Online Resource; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH). This web service compares bacterial and archaeal viruses ("phages") using their genome or proteome sequences. The results include phylogenomic trees inferred using the Genome-BLAST Distance Phylogeny method (GBDP), with branch support, as well as suggestions for the classification at the species, genus and family level. (The service can be applied to other kinds of viruses, too, but has not yet been tested in this respect.) Upload your FASTA files, GenBank files and/or GenBank accession IDs.
(Reference: JP Meier-Kolthoff & M Göker. 2017. Bioinformatics 33(21): 3396-3404).

VIRFAM

VIRFAM is dedicated to the recognition of head-neck-tail modules and of recombinase genes in phage genomes. You can use this server to search for remote homologs of specific protein families within protein sequences of bacteriophages. Input: protein sequences you're your phage; output includesd a phylogenetic tree with the placement of your virus.
(Reference: Lopes A et al. Nucleic Acids Res. (2010) 38(12): 3952-62).

VipTree

VipTree - generates a "proteomic tree" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx. The original proteomic tree concept (i.e., "the Phage Proteomic Tree") was developed by Rohwer and Edwards, 2002. A proteomic tree is a dendrogram that reveals global genomic similarity relationships between tens, hundreds, and thousands of viruses. It has been shown that viral groups identified in a proteomic tree well correspond to established viral taxonomies.
(Reference: Nishimura Y et al. (2017) Bioinformatics 33: 2379-2380).

MiGA

MiGA (Microbial Genomes Atlas) - a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts.
(Reference: Rodriguez-R et al (2018) Nucleic Acids Research 46(W1): W282-W288).

Updated: December, 2025