Presentations of Schutzenberger groups of minimal subshifts

In previous work, the first author established a natural bijection between minimal subshifts and maximal regular J-classes of free profinite semigroups. In this paper, the Sch\"utzenberger groups of such J-classes are investigated, in particular in respect to a conjecture proposed by the first author concerning their profinite presentation. The conjecture is established for all non-periodic minimal subshifts associated with substitutions. It entails that it is decidable whether a finite group is a quotient of such a profinite group. As a further application, the Sch\"utzenberger group of the J-class corresponding to the Prouhet-Thue-Morse subshift is shown to admit a somewhat simpler presentation, from which it follows that it has rank three, and that it is non-free relatively to any pseudovariety of groups.