The score is calculated as follows:
Logarithm method: score = log((number-of-players+1)/rank)
Percentile method: score = (1 - (rank / (number-of-players+1))) * 100
The score is calculated for each tournament in which a player participates and then averaged. Actually, I think the logarithm method is flawed, since it uses the "log" function, which is assumed to be log base 10, but is actually log base e.
In the works is the ability to create your own scoring formulas. It won't make it into 2.1, but it will definitely be in the following version.