Synonymous Clock Divergence
Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
Description
A simple molecular clock connects synonymous divergence with elapsed time.
A simple molecular clock connects synonymous divergence with elapsed time. Two equally evolving lineages contribute twice the per-lineage rate.1
Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
When to use Synonymous Clock Divergence
Use this for the following task: Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Synonymous Clock Divergence and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter synonymousDistance, substitutionsPerSitePerYear using the field table, then run the tool.
- Read divergenceYears, divergenceMillionYears. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| synonymousDistance | Synonymous distance | number; minimum 0 | Required |
| substitutionsPerSitePerYear | Synonymous substitution rate per site per year on each of two equally evolving branches. | number; greater than 0 | Required |
Use a nonnegative distance and positive per-site annual rate. Divide by twice the rate and convert years to million years, rejecting nonfinite results.2
years = synonymousDistance/(2 substitutionsPerSitePerYear) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| divergenceYears | Divergence years | number |
| divergenceMillionYears | Divergence million years | number |
{
"input": {
"synonymousDistance": 0.02,
"substitutionsPerSitePerYear": 1e-8
},
"output": {
"divergenceYears": 1000000,
"divergenceMillionYears": 1
}
}Limitations and assumptions
Rates are assumed equal and constant. Saturation, calibration uncertainty and lineage-specific evolution are not estimated.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Kaks Selection Screen for this operation: Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance. For a complementary task, use Synonymous Codon Sites for this operation: Count equally weighted synonymous single-base alternatives by codon position using the standard code.
Further background: Background specification: Synonymous Clock Divergence.
References
Similar or alternative tools
- Kaks Selection Screen
Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
- Synonymous Codon Sites
Count equally weighted synonymous single-base alternatives by codon position using the standard code.