codon-usage is a part of the Glimmer package, for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

codon-usage reads a multi-fasta file of gene transcripts and counts the number of occurrences of each codon (i.e., triple of nucleotides)

References:
Salzberg SL, Delcher AL, Kasif S, White O: Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998 Jan 15;26(2):544-8. [Entrez]

Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999 Dec 1;27(23):4636-41. [Entrez]