Genome Similarity (ANI)
The Genome Similarity page computes pairwise Average Nucleotide Identity (ANI) between a set of genomes and displays the results as an interactive dendrogram and matrix.
How to get there
- In the genome table, select multiple genomes (using
ShiftandCtrl), right-click and choose Show genome similarity (ANI). - From a genome detail page, use the ANI button in the toolbar.
- From the navigation bar, go to Tools → Genome Similarity (ANI).
Background processing
ANI calculations run as background jobs. After submitting, you can close the tab or navigate elsewhere; the calculation continues on the server. Results are saved and can be reopened from the Job Queues page at any time.
Engines and methods
| Engine | Method | Description |
|---|---|---|
gendiscal |
(default) | Fast minhash-based approximation of ANI. Recommended for most use cases. |
pyani-plus |
fastANI |
Sketch-based, very fast. Good for closely related genomes. |
pyani-plus |
ANIb |
Fragments compared with BLAST. Classic method. |
pyani-plus |
ANIm |
Alignment with MUMmer/nucmer. |
pyani-plus |
dnadiff |
Detailed MUMmer-based alignment statistics. |
gendiscal is the default and fastest option. The pyani-plus engine offers additional methods for more detailed or reference-grade comparisons.
Results
Results are shown in two views, switchable using the buttons above the result panel:
- Dendrogram: hierarchical clustering of genomes based on pairwise ANI distances.
- Matrix: pairwise ANI values as a color-coded grid.
Display settings
Click Display & settings to expand the options panel:
| Setting | Description |
|---|---|
| Color min (%) | ANI pairs below this threshold are shown in a neutral color; pairs at or above it are colored on the gradient. |
| ANI % | Overlay numeric ANI values on each cell. |
| Aligned fraction | Overlay the proportion of the genome covered by the alignment (matrix view only). |
| Decimals | Show 0, 1, or 2 decimal places. |
| Sort (matrix) | Order rows/columns by input order, name, species, or average ANI. |
| Cell size (matrix) | Adjust the size of each matrix cell. |
| Linkage (dendrogram) | Clustering method: average (UPGMA, recommended), ward, complete, or single. |
Exports
- Download TSV: full pairwise ANI matrix as a tab-separated file.
- Download SVG: the dendrogram as a vector image.
- View as Tree: opens the same genome set in the Trees tool, pre-loaded with the genome-similarity method.
Failed pairs
If some genome pairs fail to compute, a warning banner is shown after the job completes. Click Retry failed pairs to re-queue only the failed pairs without rerunning the entire job.