Genomic relatedness
Compute pairwise genetic distance between sequenced isolates from an alignment and group closely related isolates into clusters — a minimal, license-safe relatedness signal, not full phylogenetics.
Research question
Which isolates in this collection are genomically close enough to suggest a shared source or lineage, and what clusters does that relatedness form at a given distance threshold?
Who this is for
- Microbiome and pathogen genomics researchers screening isolate collections for relatedness
- Infectious Disease investigators who need a genomic-relatedness signal to support (not prove) outbreak-cluster and transmission-network hypotheses
- Teams who need a dependency-light relatedness method rather than a full alignment + maximum-likelihood phylogenetics pipeline
Data requirements
| Data | Required | Purpose |
|---|---|---|
| Isolate sequence alignment (FASTA-derived table, one row per isolate) | Yes | Pairwise SNP distance computation |
| SNP distance threshold | No (has a default) | Defines which pairs are grouped into the same cluster |
Workflow
Provide an isolate alignment → Run Relatedness
→ Review pairwise SNP distances and clusters
→ (Infectious Disease) link the run to exposure network / cluster investigation
Step 1 — Run Relatedness
The Relatedness analysis computes a gap/N-aware pairwise SNP distance between every pair of isolates in the alignment, then groups isolates into clusters using single-linkage clustering at the configured SNP distance threshold.
Step 2 — Review distances and clusters
The result view reports the pairwise distance matrix and the resulting clusters. This is a coarse, transparent relatedness signal — full multiple-sequence alignment (MAFFT) and maximum-likelihood phylogenetics (IQ-TREE) are later work, not what this pipeline does today.
Step 3 — Cross-area use (optional)
Infectious Disease can link a completed Relatedness run into its exposure-network and cluster-investigation analyses, mapping episodes to isolates by sample ID and annotating candidate epidemiological links with true pairwise genomic distance instead of a coarse shared-lineage proxy.
Expected outputs
- Pairwise SNP distance matrix across isolates
- Single-linkage clusters at the configured distance threshold
- A run artifact that Infectious Disease can reference by run ID for cross-area genomic support
Important caveats
Genomic relatedness is a supporting signal for outbreak and transmission hypotheses, never proof of transmission by itself. It does not replace full phylogenetic inference or formal outbreak genomics review.