I used to run ggsearch36 from the fasta package for NW alignment of proteins and now need to switch to needle from emboss, as ggsearch36 skips low-scoring alignments, whereas needle can return all.

I'm looking for the correct configuration to make needle return the same alignment as ggsearch36. I tried adjusting the matrix, the gap penalties and the end gap penalties, but nothing seems to make the two programs agree. Is there a parameter set that can achieve this?