Description
Return equal-rates four-state substitution probabilities.
Biological growth and substitution models encode specific assumptions about rates, interactions and state spaces. Evaluating their formula at one supplied state can illustrate the model without fitting parameters, integrating a trajectory or establishing that its assumptions hold for real observations.
Return equal-rates four-state substitution probabilities.
When to use this tool
Use Phylogeny Edge Transition Probability Term when evaluating the stated biological rate or substitution-model term under its declared assumptions.
How to use the tool and how it works
- Enter substitutionRate, branchDuration. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read stayProbability, oneOtherBaseProbability. Use the output convention below.
Return equal-rates four-state substitution probabilities. Require substitutionRate/branchDuration >= 0; stay = 1/4+3*exp(-4*rate*time/3)/4 and oneOtherBaseProbability = (1-exp(-4*rate*time/3))/4.1
JC69 assumes equal base frequencies and substitution rates; unequal-frequency or rate models require different transition formulas.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| substitutionRate | Expected total substitutions per site per matching time unit, under the equal-rates JC69 normalization. | Required. Finite number; minimum 0. |
| branchDuration | Branch Duration | Required. Finite number; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| stayProbability | Stay Probability | Required. Finite number. |
| oneOtherBaseProbability | Probability for one particular alternative base, not the sum of all three alternatives. | Required. Finite number. |
{
"input": {
"substitutionRate": 0,
"branchDuration": 2
},
"output": {
"stayProbability": 1,
"oneOtherBaseProbability": 0
}
}Limitations and assumptions
- Rate is total expected substitutions per site/time under the JC69 convention; the other-base probability is for each one of three alternatives.
- 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
Fit and validate an appropriate complete model against relevant data, with parameter, time-unit and numerical-error checks for biological inference.
References
-
Calculation and input contract: computational-biology/phylogeny-edge-transition-probability-term — tool.io
-
Substitution models: DNA models — IQ-TREE developers
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