Description
Return -½ln(1-2P-Q)-¼ln(1-2Q) and both positive logarithm margins.
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 -½ln(1-2P-Q)-¼ln(1-2Q) and both positive logarithm margins.
When to use this tool
Use Kimura Two Parameter Distance Domain Gap when you need the stated sequence-distance or codon-opportunity term.
How to use the tool and how it works
- Enter transitionFraction, transversionFraction. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read distance, transitionLogMargin, transversionLogMargin. Use the output convention below.
Require nonnegative transition/transversion fractions with 2P+Q<1 and 2Q<1. Return -½ln(1-2P-Q)-¼ln(1-2Q) and both positive logarithm margins.1
Kimura two-parameter distance distinguishes transition and transversion proportions under equal equilibrium nucleotide frequencies.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| transitionFraction | Fraction P of compared sites differing by transitions. | Required. Finite number; minimum 0. |
| transversionFraction | Fraction Q differing by transversions. | Required. Finite number; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| distance | Distance in the stated common unit and geometric model. | Required. Finite number. |
| transitionLogMargin | Transition Log Margin | Required. Finite number. |
| transversionLogMargin | Transversion Log Margin | Required. Finite number. |
{
"input": {
"transitionFraction": 0.1,
"transversionFraction": 0.1
},
"output": {
"distance": 0.23412335979791865,
"transitionLogMargin": 0.7000000000000001,
"transversionLogMargin": 0.8
}
}Limitations and assumptions
- Fractions are mismatch proportions, not counts. This is the Kimura two-parameter model with its substitution assumptions, not a sequence alignment or saturation correction beyond its domain.
- 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
- Jukes Cantor Distance Domain Margin
Return -¾ln(1-4p/3) and 0.75-p as saturationMargin.
- Phylogenetic Tip Date Root Distance Gap Tool
Calculate phylogenetic tip date root distance gap from explicit caller-supplied inputs.