Table 1.

Available tools for calculating codon usage metrics

Tool	Functionality	Availability	URL (citation)
CAIcal	Calculates CAI for provided gene sequences and codon usage tables	Web	http://genomes.urv.es/CAIcal/ [32]
CoCoPUTs	Database of codon-pair and dinucleotide statistics for all genomes in GenBank	Web	https://hive.biochemistry.gwu.edu/review/codon2 [31]
CodonW	Calculates codon metrics for user-selected gene set and correspondence analysis	Local installation	https://sourceforge.net/projects/codonw/
coRdon	Calculates codon bias statistics	R package	https://www.bioconductor.org/packages/devel/bioc/vignettes/coRdon/inst/doc/coRdon.html
COUSIN	Calculates codon usage for user-supplied sequences	Web or install	http://cousin.ird.fr/index.php [34]
EncPrime	Calculates ENC metric	Local installation	https://github.com/jnovembre/ENCprime
GCUA	Calculates codon metrics for user-selected gene set and correspondence analysis	Local installation	http://mcinerneylab.com/software/gcua/
HEG-DB	Database of CAI index of HEGs for 200 genomes	Web	http://genomes.urv.cat/HEG-DB/ [33]
SMS	Calculates codon metrics for user-supplied sequences	Web	https://www.bioinformatics.org/sms2/codon_usage.html