Primary reference for PASSML:

Liò, P., Goldman, N., Thorne, J.L., and Jones, D.T. (1998)
PASSML: combining evolutionary inference and protein secondary structure prediction.
Bioinformatics 14:726-733.

Primary reference for PASSML_TM:

Liò, P., and Goldman, N. (1999)
Using protein structural information in evolutionary inference: transmembrane proteins
Molecular Biology and Evolution 16: 1696-1710.