Description
Calculate expected substitutions from supplied branch duration, eligible sites and per-site-time rate.
Evolutionary summaries depend on sampled sequences/populations, reference states, ploidy, time units and stochastic assumptions. A mixture expectation differs from a drift simulation, and a callable-allele denominator differs from an individual count. Labels and local tree conditions do not reconstruct ancestry or establish a biological mechanism.
Calculate expected substitutions from supplied branch duration, eligible sites and per-site-time rate.
When to use this tool
Use Branch Site Substitution Opportunity Term when checking the stated evolutionary record, reference, expectation or scale convention.
How to use the tool and how it works
- Enter branchDuration, eligibleSites, suppliedRatePerSiteTime. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read expectedSubstitutions. Use the output convention below.
Require nonnegative branch duration, whole eligible sites>=0 and nonnegative rate per site-time. Multiply all three for expectedSubstitutions.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| branchDuration | Branch Duration | Required. Finite number; minimum 0. |
| eligibleSites | Eligible Sites | Required. Safe integer; minimum 0. |
| suppliedRatePerSiteTime | Supplied Rate Per Site Time | Required. Finite number; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| expectedSubstitutions | Expected Substitutions | Required. Finite number. |
{
"input": {
"branchDuration": 2,
"eligibleSites": 100,
"suppliedRatePerSiteTime": 0.01
},
"output": {
"expectedSubstitutions": 2
}
}Limitations and assumptions
- An expectation may be fractional; no substitutions are sampled, sites examined or molecular-rate model fitted.
- 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 verified samples/references and appropriate complete phylogenetic, population-genetic or statistical models for actual biological inference and uncertainty.
References
Similar or alternative tools
- Migration Drift Generation Expectation
Calculate an expected allele frequency after deterministic migration mixing.
- Population Transfer Dilution Count
Calculate expected transferred and remaining population counts under a supplied transfer fraction.