Distance Cut

There is some evidence that distance computations are unreliable when they are near 1. This is illustrated by lack of correlation between Blast and Needleman Wunsch for Blast distances above 0.9.

So in some dimension reduction runs we remove terms where distances are larger than "Distance Cut" which value is specified on input. Remember we are minimizing sum of N(N-1)/2 terms
(distance between i and j - Euclidean distance between mapped i and j)^2
So we drop terms where distance between i and j> Distance Cut. Typically any point i and j are still left with some distances less than cut and so you can determine mapping.
For Blast sometimes distances are not calculated and those terms are also left out of sum

Manxcat is only dimension  reduction program that allows missing distances. It removes any point that has less than or equal Linkcut valid distances. Linkcut is defaulted to 5