A Dirichlet mixture file specifies residues' tendencies to align with one another, and is the basis for scoring columns of aligned residues. The format is identical to that of UCSC Dirichlet mixtures. For examples, see recode3.20comp (copied from UCSC) and glam_tfbs.1comp in the GLAM2 examples directory.
The GLAM2 programs only read lines beginning with Mixture= or Alpha=. Mixture= is followed by a number giving the weight of that mixture component: these weights should sum to 1. Alpha= is followed by a list of numbers giving the pseudocounts for that mixture component, as many as there are symbols in the alphabet. The first number after Alpha= is the sum of the pseudocounts, and is in fact ignored by the GLAM2 programs.
The pseudocounts should be in the same order as the alphabet symbols. For the n (nucleotide) alphabet, this is: acgt. For the p (protein) alphabet, this is: ACDEFGHIKLMNPQRSTVWY.
If no Dirichlet mixture file is specified, the default is to use recode3.20comp for the p (protein) alphabet, glam_tfbs.1comp for the n (nucleotide) alphabet, and a uniform prior for user-specified alphabets.