How do I quickly run through all possible merger outputs?

Question

[lzbenicmi]

I'm trying to find a consensus sequence using a handful of different reads in a fasta file. I was instructed to use Merger, but I can't make it go through all the possible alignments quick enough and I don't really know what I'm doing.

I have 8 reads, and I need a way to efficiently run through all the possible pairwise comparisons + reverse compliments to create a 50 nucleotide consensus sequence. Is there any way to get Merger to run through all the possibilities at once, or code I can write that will run it for me? I realize this is kind of a noob question.