Codon usage with unknown/unspecified Nucleotides

Hi,

I am perfoming Codon usage analysis with coRdon package, and I wondering about how this package or other bioinformatics tool handle sequences with a significant amount of “Ns”, I failed to find any tip about it or even a deep discussion.

In addition to that, what would be the best approach for this situation? Simply trimmer codons with “N” nucleotides? Assuming that maybe 1~5% of candidate sequences length contain unknow nucleotides, that would be a bad noise in the analysis?

Thanks in advance for any insight!