sumatra - fast and exact comparison and clustering of sequences

       Sumatra  computes  all  the pairwise LCS (Longest Common Subsequence) scores of one nucleotide dataset or
       between two nucleotide datasets.

       sumatra - fast and exact comparison and clustering of sequences

-h     [H]elp - print <this> help

       -l     Reference sequence length is the shortest.

       -L     Reference sequence length is the largest.

       -a     Reference sequence length is the alignment length (default).

       -n     Score is normalized by reference sequence length (default).

       -r     Raw score, not normalized.

       -d     Score is expressed in distance (default: score is expressed in similarity).

       -t##.##
              Score threshold. If the score is normalized and  expressed  in  similarity  (default),  it  is  an
              identity,  e.g. 0.95 for an identity of 95%. If the score is normalized and expressed in distance,
              it is (1.0 - identity), e.g. 0.05 for an identity of 95%.  If the  score  is  not  normalized  and
              expressed  in  similarity, it is the length of the Longest Common Subsequence. If the score is not
              normalized and expressed in distance, it is (reference length - LCS length).
              Only sequence pairs with a similarity above ##.## are printed. Default: 0.00 (no threshold).

       -p##  Number of threads used for computation (default=1).

       -g     n's are replaced with a's (default: sequences with n's are discarded).

       -x     Adds four extra columns with the count and length of both sequences.

       dataset1
              (First argument) the nucleotide dataset to analyze

       dataset2
              (Second argument) optionally the second nucleotide dataset

       Results table description
       column 1 : Identifier sequence 1
       column 2 : Identifier sequence 2
       column 3 : Score
       column 4 : Count of sequence 1  (only with option -x)
       column 5 : Count of sequence 2  (only with option -x)
       column 6 : Length of sequence 1 (only with option -x)
       column 7 : Length of sequence 2 (only with option -x)

http://metabarcoding.org/sumatra

sumatra 1.0.03                                     August 2015                                        SUMATRA(1)

sumatra[options]<dataset1>[dataset2]