Less than theoratical number of pair using pairwise.seqs


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.


I think I found out what is wrong… I set cutoff=0.03, so any distance that is larger than 0.03 was deleted.