We describe an algorithm that uses Stallings' folding technique to decompose an element of $Aut(F_n)$ as a product of Whitehead automorphisms (and hence as a product of Nielsen transformations.) We use this to give an alternative method of finding a finite generating set for the subgroup of $Aut(F_n)$ that fixes a subset $Y$ of the basis elements, and the subgroup that fixes each element of $Y$ up to conjugacy. We show that the intersection of this latter subgroup with $IA_n$ is also finitely generated.

12 pages, 4 figures. Final draft. To appear in The Quarterly Journal of Mathematics