Needing Advice: Best algo(s) for distance based on "proportion of shared substrings"

[davidmcnabnz]

Hi there, I'm just getting started with string similarity processing.
In my application, I need to compare short-ish strings of length 25-300 characters, and I need the 'distance between any two' metric to reward things like:

1. Proportion of each string which is shared substrings, and
2. Sizes of shared substrings, especially relative to the lengths of the strings being compared

Any suggestions, among the wealth of algorithms and modes supported in this package?

Cheers
David