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

alf 1.1.10 [tarball]                                                                                      ALF(1)