I would like to compare the amino acid and the codon usage content between two organisms. What statistical test would be appropriate for this purpose? And what are the inputs needed?
I recommend that you study the work of Jean Lobry, who has done a lot of work in this area.
Search PubMed for "Lobry JR[AU]" or see his partial list of publications.
He has also written an R package called seqinR which contains many methods for statistical analysis of sequences, including composition. Read the documentation, in particular chapter 9 on multivariate analysis.
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version 2.3.6
Could be a little more specific? What are you looking for? Just that two organisms have a diference in codon content?
+1 for a question of interest! Please do provide us with more details about your data, goals, explored methodologies. You will get more relevant and detailed answers :)