Description
Return change/site dN and dS and their ratio.
Sequence-derived quantities depend on aligned observations, callable sites and a stated substitution or codon model. A count ratio or one site's opportunity is distinct from a corrected evolutionary distance or statistical evidence of selection.
Return change/site dN and dS and their ratio.
When to use this tool
Use dN/dS One Codon Site Count Term when you need the stated sequence-distance or codon-opportunity term.
How to use the tool and how it works
- Enter nonsynonymousChanges, nonsynonymousSites, synonymousChanges, synonymousSites. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read dN, dS, ratio. Use the output convention below.
Require nonnegative nonsynonymous changes and positive nonsynonymous sites, synonymous changes and synonymous sites. Return change/site dN and dS and their ratio.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| nonsynonymousChanges | Nonsynonymous Changes | Required. Finite number; minimum 0. |
| nonsynonymousSites | Nonsynonymous Sites | Required. Finite number; strictly above 0. |
| synonymousChanges | Synonymous Changes | Required. Finite number; strictly above 0. |
| synonymousSites | Synonymous Sites | Required. Finite number; strictly above 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| dN | D N | Required. Finite number. |
| dS | D S | Required. Finite number. |
| ratio | Dimensionless ratio under the numerator/denominator convention above. | Required. Finite number. |
{
"input": {
"nonsynonymousChanges": 12,
"nonsynonymousSites": 600,
"synonymousChanges": 4,
"synonymousSites": 200
},
"output": {
"dN": 0.02,
"dS": 0.02,
"ratio": 1
}
}Limitations and assumptions
- This is a raw supplied-count normalization without multiple-hit correction, codon model or statistical selection test. Zero synonymous changes is rejected rather than assigned infinite ratio.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use a complete sequence-analysis method with an appropriate alignment, genetic code and model. Review gaps, missingness, multiple substitutions, saturation and uncertainty before biological interpretation.
References
Similar or alternative tools
- Codon Sites Zero Denominator
Divide by sites when positive, otherwise return zero with defined false.
- Codon Synonymous Site Mask
Mark neighbors matching its nonexcluded amino-acid token and sum their weights by changed position and overall.