Hi,
I was using pairwise.seqs to get the pairwise distance.
I have 26059 unique sequences, which theoretically will result in 339,522,711 pair-ed distance, right?
But I counted the line in the .dist file and it was 2624643. Does it mean that if the distance is 0, it is omitted?
I also tested with a 21 sequences fasta file, and the .dist file turned out to contain 210 lines, which is equal to the theoretical number.
Thanks!