GCUA:General Codon Usage Analysis

GCUA:General Codon Usage Analysis is a handy, easy to use, Java based application specially designed to perform various tasks that are of use for evaluating codon usage in a set of genes. You can get it to do some simple things like calculate the number of observations of a particular codon in a gene. Or you can do the same thing for the combined dataset. You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole). The program also produces a distance matrix based on the similarity of codon usage in genes.

However, the most important feature of the program is its ability to use multivariate analysis to look at variation in codon usage amongst genes. Although it is popular to say that an organism has a particular codon usage, it is now known that an organisms genes might have more than one codon usage pattern and it is usually only by using a multivariate analysis method that it is possible to ascertain the kinds of variation contained within the data.