pfmake is part of the pftools package, a collection of tools making use of generalised profiles for sequence analysis.

pfmake generates a PROSITE profile from a multiple sequence alignment using methods described by Gribskov et al.(1990), Luethyet al. (1994), and Thompson et al. (1994), with modifications to exploit the features of the new profile format.

References:
Bucher P, Karplus K, Moeri N & Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20:3-24.

Gribskov M, Luethy R & Eisenberg D (1990). Profile analysis. Meth. Enzymol. 183:146-159.

Luethy R, Xenarios I & Bucher P (1994). Improving the sensitivity of the sequence profile method. Prot. Sci.3:139-146.

Thompson JD, Higgins DG & Gibson TJ (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 10:19-29.