Codon Usage Bias (CUB) for 1,434 species from 8 life domains

The main file in this record was obtained within R (version 4.3.2 (2023-10-31)) using our package "Shannon.codon" (An R package for the analysis of codon frequencies version 1.5) and results using that package were published in "Sampling informational properties of codon usage through the tree of life". The files in this record are: 1 - "cub.RData"After loading with load("cub.RData") you will have the object "cub" in your R environment. Let's see the comment of that file: > comment(cub)"Data frame of Codon Usage Bias (CUB) for 1,434 species from 8 life domains. Each row was obtained with the codon.bias function of the Shannon.codon package; the command to obtain each row of cub was cub[i,] <- codon.bias(codon.raw.freq[i,], only.main=T)$CodBias.aa The names of the 19 columns correspond to the amino acids (aa) which are coded by at least two codons. The first two letters of the row names attributes of cub identify the species of the organism; say, An (Animal 652), Ar (Archaea 435), Eb (Enterobacteriaceae 126), Fu (Fungus 71), Ob (Other Bacteria 3), Pl (Plant 122), Pr (Protist 4) or Vi (Virus 21). Natural numbers after the two letters give the order of the species within group. The order of cub rows is the same than in the species data.frame within the Shannon.codon package, thus, you can obtain the scientific name from species$Species. 2 - "cub.txt"This file has the same information than object "cub" (in file "cub.RData") but the values are segregated by tabs for compatibility. 3 - "aa.properties.RData" Properties of amino acids (aa). After doing load("aa.properties.RData") you will have the object "aa.properties" in your environment. See the "README.txt" file included in this record for details.