Not sure what the abbreviation is actually supposed to mean, but it directly translates into the retree (tree iteration) option, i.e. NS2 is --retree 2. This table shows a list of all names and commands that are actually used.
Using the FFT algorithm and the normalized similarity matrix described
above, input sequences are progressively aligned following the
branching order of sequences in the guide tree. This method is
hereafter referred to as FFT-NS-1.
So... NS means normalized similarity matrix.
I think what it is maybe similar to Gramian matrix in linear algebra.