Codon Usage Table Tools-lery.
‘cuttlery’ is a package for determining the codon usage table of input sequences. Instead of calculating an absolute codon usage frequency for all observed genes as other packages do, cuttlery handles codon usage frequency as a distribution for each codon. The cuttlery package also contains tools for plotting codon usage information, calculating if an unknown ORF is likely to belong to coding or noncoding sequence, calculating nucleotide diversity of protein alignments and plotting the results, as well as looking for synonymous and nonsynonymous mutation heterogeneity in protein alignments. https://github.com/conchoecia/cuttlery
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