Clade Signature Support
Score caller-defined multi-mutation clade signatures, retaining ambiguous matches rather than asserting lineage assignment.
Description
Count exact mutation-label matches against supplied clade signatures and identify threshold-qualified candidates.
A clade groups related viral genomes, and a mutation signature is a chosen set of labels associated with a candidate group. Sequence-based lineage designation involves broader evidence than a simple label match; formal schemes maintain their own designation processes.1
This tool compares your observed mutation labels with your own candidate signatures. It divides the number of matched signature labels by the number of labels in that signature. The resulting fraction is a coverage score, not a probability that a sample belongs to the clade.
Each signature is a semicolon-separated string paired with a clade name. A candidate qualifies when its fraction is at least the supplied threshold. Ambiguous means more than one candidate qualifies; zero candidates also gives ambiguous false.
When to use Clade Signature Support
Use it to audit a transparent, caller-defined mutation checklist or compare candidate support before a fuller sequence or phylogenetic analysis.
How to use Clade Signature Support and interpret its calculation
- Enter observedMutations as a list of exact labels, and aligned nonempty cladeNames and signatureSets lists.
- Separate signature labels with semicolons. Keep clade names unique and each signature nonempty, without duplicate labels.
- Choose minimumMatchFraction between 0 and 1, run the comparison, and read matchingClades alongside matchFractions and ambiguous. Inspect unmatched labels and sequence coverage separately.
The implementation builds a set from observed labels, so repeated observations do not add support. It splits each signature at semicolons and trims the signature tokens before checking membership. Comparisons are case-sensitive; observed labels are not automatically trimmed.
match fraction = count(signature labels present in observed set) / count(signature labels); qualifies = fraction ≥ threshold Scores and qualified names retain the candidate input order. Extra observed mutations do not penalize a score.
{
"input": {
"observedMutations": [
"A",
"B"
],
"cladeNames": [
"X",
"Y"
],
"signatureSets": [
"A;B",
"B;C"
],
"minimumMatchFraction": 1
},
"output": {
"matchFractions": [
1,
0.5
],
"matchingClades": [
"X"
],
"ambiguous": false
}
}An empty observed list is accepted and gives zero support for every candidate. Threshold zero qualifies every candidate, even without observations. Empty signature tokens and duplicate trimmed signature labels are rejected.
Limitations and assumptions
Absent observations can reflect missing coverage rather than a reference allele. The tool does not distinguish those situations, call mutations, align sequences, weight sites, or account for shared signatures and homoplasy.
No clade definitions are bundled or updated, and no official lineage assignment is made. A single qualified candidate is not proof of a correct assignment; always inspect matchingClades when interpreting ambiguous false.
Alternative or Complementary methods
Use sequence-distance or phylogenetic methods for broader relatedness evidence. A lineage-label format check can catch naming problems, but it cannot verify an assigned lineage biologically.
References
-
Pango lineage designation repository: README — Pango Network
Similar or alternative tools
- Genomic Distance Clusters
Cluster genomes from supplied pairwise distances rather than signature labels.
- Lineage Format Audit
Check the syntax of supplied lineage labels without validating ancestry.