Description
Multiply elapsed years by rate and subtract from observed root distance.
Evolutionary time and branch length are linked through a supplied clock or calibration. A unit conversion, path sum or residual assumes the underlying tree and rate model rather than recovering them from biological data.
Multiply elapsed years by rate and subtract from observed root distance.
When to use this tool
Use Phylogenetic Tip Date Root Distance Gap when you need one branch-time, path or calibration term.
How to use the tool and how it works
- Enter tipYear, rootYear, rootDistance, clockRate. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read elapsedYears, expectedDistance, residual. Use the output convention below.
Require tipYear at least rootYear, nonnegative root distance and positive clockRate. Multiply elapsed years by rate and subtract from observed root distance.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| tipYear | Tip Year | Required. Finite number. |
| rootYear | Root Year | Required. Finite number. |
| rootDistance | Root Distance | Required. Finite number; minimum 0. |
| clockRate | Clock Rate | Required. Finite number; strictly above 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| elapsedYears | Elapsed Years | Required. Finite number. |
| expectedDistance | Expected Distance | Required. Finite number. |
| residual | Residual | Required. Finite number. |
{
"input": {
"tipYear": 2020,
"rootYear": 2000,
"rootDistance": 0.025,
"clockRate": 0.001
},
"output": {
"elapsedYears": 20,
"expectedDistance": 0.02,
"residual": 0.005000000000000001
}
}Limitations and assumptions
- Clock rate is distance units/year on the same branch basis. This one residual does not fit a clock, date a tree or quantify calibration uncertainty.
- 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 phylogenetic or dating method with the relevant sequence, fossil and rate evidence. Verify topology, branch units, calibration assumptions and uncertainty separately.
References
Similar or alternative tools
- Molecular Clock Branch Time Factor
Divide distance by rate, with an additional factor two when twoLineages.
- Phylogenetic Node Age Branch Residual
Return parentAge-childAge and its residual against branch duration, plus consistentOrder for parent at least child.