We have developed coRdon, an R package for the analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences.
coRdon can be used to easily calculate several different measures of codon usage (CU) bias and CU-based predictors of gene expressivity, including ENC, CAI, B, SCUO and MILC.
The statistics can be calculated for sequences originating from different genomes, and even metagenomes, as we have shown in the example here, because the calculations do not rely on the predefined reference gene set - rather, the reference genes or codon usage values are specified by the user.
coRdon can also be used to perform CU-based gene set enrichment analysis for annotated DNA sequences.
Finally, several different methods for visualisation of CU and enrichment analysis results are also implemented.