We study two problems in Nielsen fixed point theory using Artin's braid groups and the Nielsen–Thurston classification of surface homeomorphismsup to isotopy. The first is that of distinguishing Reidemeister classes of free group automorphisms realized by a braid (and thus induced by homeomorphismsof the 2-disc relative to a finite invariant set), for which we give a necessary and sufficient condition in terms of a conjugacy problem in the braid group. Consequently, one may use any braid conjugacy invariant (those of Garside's algorithm, linking numbers, topological entropy, etc.) and any link invariant (Alexander polynomial, splittability, etc.) to distinguish Reidemeisterclasses, giving much stronger criteria than those already known. The second problem is that of deciding when two fixed points of a surface homeomorphismbelong to the same Nielsen fixed point class. We give two criteria, the first in terms of certain reducing curves which can be checked using the Bestvina–Handel algorithm, the second using the multi-variable Alexander polynomial of a link associated with the suspension of the homeomorphism. Finally we consider generalizations of Sharkovskii's theorem on the coexistence of periodic orbits of interval maps to homeomorphismsof the 2-disc. We show that for each n⩾5 there exists a pseudo-Anosovorientation-preservinghomeomorphismof the 2-disc relative to a periodic orbit of period n that does not have periodic orbits of all periods, with an analogous result for the 2-sphere.