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       alf - Alignment free sequence comparison


       alf [OPTIONS] -i IN.FASTA [-o OUT.TXT]


       Compute  pairwise  similarity  of  sequences  using alignment-free methods in IN.FASTA and
       write out tab-delimited matrix with pairwise scores to OUT.TXT.


       -h, --help
              Display the help message.

              Display version information.

       -v, --verbose
              When given, details about the progress are printed to the screen.

   Input / Output:
       -i, --input-file INPUT_FILE
              Name of the multi-FASTA  input  file.  Valid  filetypes  are:  .sam[.*],  .raw[.*],
              .gbk[.*],  .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*],
              .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz,  bz2,
              and bgzf for transparent (de)compression.

       -o, --output-file OUTPUT_FILE
              Name  of  the  file  to which the tab-delimtied matrix with pairwise scores will be
              written to.  Default is to write to stdout. Valid filetype is: .alf[.*], where * is
              any of the following extensions: tsv for transparent (de)compression.

   General Algorithm Parameters:
       -m, --method STRING
              Select method to use. One of N2, D2, D2Star, and D2z. Default: N2.

       -k, --k-mer-size INTEGER
              Size of the k-mers. Default: 4.

       -mo, --bg-model-order INTEGER
              Order of background Markov Model. Default: 1.

   N2 Algorithm Parameters:
       -rc, --reverse-complement STRING
              Which  strand to score.  Use both_strands to score both strands simultaneously. One
              of input, both_strands, mean, min, and max. Default: input.

       -mm, --mismatches INTEGER
              Number of mismatches, one of 0 and 1.  When 1 is used, N2 uses the  k-mer-neighbour
              with one mismatch. Default: 0.

       -mmw, --mismatch-weight DOUBLE
              Real-valued weight of counts for words with mismatches. Default: 0.1.

       -kwf, --k-mer-weights-file OUTPUT_FILE
              Print  k-mer  weights  for every sequence to this file if given. Valid filetype is:


       For questions or comments, contact:
              Jonathan Goeke <>

       Please reference the following publication if you used ALF  or  the  N2  method  for  your
              Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. Estimation of
              Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts.
              Bioinformatics (2012).

       Project Homepage: