NAME

       alf - Alignment free sequence comparison

SYNOPSIS

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

DESCRIPTION

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

OPTIONS

       -h, --help
              Display the help message.

       --version
              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:
              .txt.

CONTACT AND REFERENCES

       For questions or comments, contact:
              Jonathan Goeke <goeke@molgen.mpg.de>

       Please reference the following publication if you used ALF  or  the  N2  method  for  your
       analysis:
              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:
              http://www.seqan.de/projects/alf