Mismatch Calculator

Do it-easy calculator for converting substitution rates in coaelescence (or time since expansion) estimation.

The following tool is provided for use with the mismatch distribution calculation in order to produce a range a values for the "time since expansion" calculation, regardless of what form you have for the substitution (or divergence) rate. The tool can also be used as a "rate" converter for various forms of substitution (or divergence) rates regardless of their intended use.

The "mismatch distribution analysis" or "analysis of pairwise mismatches" provides a means of detecting the genetic signal of a historical demographic expansion in a species or population. It allows the estimation of the time since expansion by using the formula t=τ/2u where τ is a unit of mutational time and u is the cumulative substitution rate per generation across the DNA fragment under study.

To accommodate the heterogeneous forms in which substitution or divergence rates are reported in literature, the tool allows the use of four different formats:

Divergence rate - %Div/MY = Percent divergence per million years: The percent by which the DNA fragment under study of will differ between two diverging lineages per million years. use this and continue
Substitution rate - Subst/linage/Site/MY = The absolute probability that a substitution will occur at a specific site in the gene of interest, within a lineage per million years. use this and continue
Substitution rate - Subst/lineage/Site/Gen (μ): The probability that a substitution will occur at a specific site in the gene of interest during one generation. This is the most common way that substitution rate is reported in academic literature. use this and continue
Substitution rate - Cumulative Subst/lineage/Gen (u): The probability that a substitution will occur anywhere in the gene of interest during one generation. This is the unit called for in the mismatch formula. use this and continue