Tamuras 3-parameter model corrects for multiple hits, taking into account the differences in transitional and transversional rates and the G+C-content bias (1992). It assumes an equality of substitution rates among sites. When the G+C-contents are different between the sequences, the modified formula (Tamura and Kumar 2002) relaxes the assumption of substitution pattern homogeneity.
The Tamura 3-parameter model
MEGA provides facilities for computing the following quantities:
|
Quantity |
Description |
|
d: Transitions & Transversions |
Number of nucleotide substitutions per site. |
|
s: Transitions only |
Number of transitional substitutions per site. |
|
v: Transversions only |
Number of transversional substitutions per site. |
|
R = s/v |
Transition/transversions ratio. |
|
L: No of valid common sites |
Number of sites compared. |
Formulas for computing these quantities are as follows:
Distances
where P and Q are the proportion of sites with transitional and transversional differences, respectively, and
The variances can be estimated by the bootstrap method. .