Is it possible to run the EMBOSS cusp program so that it gives output (codon usage) for each individual sequence in a list of FASTA sequences? In the default version it analyzes all sequences together.
If multiple sequences are input then the statistics are given for all of the sequences together, not individually.
So no, this is not an option in the command-line arguments. You will have to split your multiple FASTA sequence file into individual sequences. Lots of ways to do that, one of them is EMBOSS seqretsplit.