Description
Return -¾ln(1-4p/3) and 0.75-p as saturationMargin.
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 -¾ln(1-4p/3) and 0.75-p as saturationMargin.
When to use this tool
Use Jukes Cantor Distance Domain Margin when you need the stated sequence-distance or codon-opportunity term.
How to use the tool and how it works
- Enter mismatchFraction. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read distance, saturationMargin. Use the output convention below.
Require mismatchFraction in [0, 0.75). Return -¾ln(1-4p/3) and 0.75-p as saturationMargin.1
Jukes-Cantor distance assumes equal nucleotide frequencies and equal substitution rates. Its logarithm requires mismatch proportion below three quarters.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| mismatchFraction | Mismatch Fraction | Required. Finite number; minimum 0; strictly below 0.75. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| distance | Distance in the stated common unit and geometric model. | Required. Finite number. |
| saturationMargin | Saturation Margin | Required. Finite number. |
{
"input": {
"mismatchFraction": 0.3
},
"output": {
"distance": 0.383119217824493,
"saturationMargin": 0.45
}
}Limitations and assumptions
- The Jukes-Cantor model assumes equal nucleotide frequencies and equal substitution rates. It does not align sequences, handle gaps or give finite distance at the saturation boundary.
- 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
-
Calculation and input contract: evolutionary-biology/jukes-cantor-distance-domain-margin — tool.io
-
Distance estimation: nucleotide substitution models — MEGA software authors
Similar or alternative tools
- Kimura Two Parameter Distance Domain Gap
Return -½ln(1-2P-Q)-¼ln(1-2Q) and both positive logarithm margins.
- Allele Count Frequency Residual Tool
Calculate allele count frequency residual from explicit caller-supplied inputs.