We present a new technique for computing permutation polynomials based on equivalence relations. The equivalence relations are defined by expanded normalization operations and new functions that map permutation polynomials (PPs) to other PPs. Our expanded normalization applies to almost all PPs, including when the characteristic of the finite field divides the degree of the polynomial. The equivalence relations make it possible to reduce the size of the space, when doing an exhaustive search. As a result, we have been able to compute almost all permutation polynomials of degree $d$ at most 10 over $GF(q)$, where $q$ is at most 97. We have also been able to compute nPPs of degrees 11 and 12 in a few cases. The techniques apply to arbitrary $q$ and $d$. In addition, the equivalence relations allow the set all PPs for a given degree and a given field $GF(q)$ to be succinctly described by their representative nPPs. We give several tables at the end of the paper listing the representative nPPs (\ie the equivalence classes) for several values of $q$ and $d$. We also give several new lower bounds for $M(n,D)$, the maximum number of permutations on $n$ symbols with pairwise Hamming distance $D$, mostly derived from our results on PPs.