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       stellar - the SwifT Exact LocaL AligneR


       stellar [OPTIONS] <FASTA FILE 1> <FASTA FILE 2>


       STELLAR  implements the SWIFT filter algorithm (Rasmussen et al., 2006) and a verification
       step for the SWIFT hits  that  applies  local  alignment,  gapped  X-drop  extension,  and
       extraction of the longest epsilon-match.

       Input  to  STELLAR  are  two files, each containing one or more sequences in FASTA format.
       Each sequence from file 1 will be compared to each sequence in file 2. The sequences  from
       file 1 are used as database, the sequences from file 2 as queries.

       (c) 2010-2012 by Birte Kehr


               Valid filetypes are: .fasta and .fa.

               Valid filetypes are: .fasta and .fa.


       -h, --help
              Display the help message.

              Display version information.

   Main Options:
       -e, --epsilon DOUBLE
              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength INTEGER
              Minimal length of epsilon-matches. In range [0..inf]. Default: 100.

       -f, --forward
              Search only in forward strand of database.

       -r, --reverse
              Search only in reverse complement of database.

       -a, --alphabet STRING
              Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of dna,
              dna5, rna, rna5, protein, and char.

       -v, --verbose
              Set verbosity mode.

   Filtering Options:
       -k, --kmer INTEGER
              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriod INTEGER
              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLength INTEGER
              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCut DOUBLE
              k-mer overabundance cut ratio. In range [0..1]. Default: 1.

   Verification Options:
       -x, --xDrop DOUBLE
              Maximal x-drop for extension. Default: 5.

       -vs, --verification STRING
              Verification strategy: exact or bestLocal or bandedGlobal One of exact,  bestLocal,
              and bandedGlobal. Default: exact.

       -dt, --disableThresh INTEGER
              Maximal  number  of  verified  matches  before disabling verification for one query
              sequence (default infinity). In range [0..inf].

       -n, --numMatches INTEGER
              Maximal number of kept matches per  query  and  database.  If  STELLAR  finds  more
              matches, only the longest ones are kept. Default: 50.

       -s, --sortThresh INTEGER
              Number  of  matches  triggering  removal  of duplicates. Choose a smaller value for
              saving space. Default: 500.

   Output Options:
       -o, --out OUTPUT_FILE
              Name of output file. Valid filetypes are: .txt and .gff. Default: stellar.gff.

       -od, --outDisabled OUTPUT_FILE
              Name of output file for disabled query sequences. Valid  filetypes  are:  .sam[.*],
              .raw[.*],  .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*],
              .fa[.*], and .bam, where * is any of the following extensions: gz,  bz2,  and  bgzf
              for transparent (de)compression. Default: stellar.disabled.fasta.


       Kehr,  B.,  Weese,  D.,  Reinert,  K.:  STELLAR:  fast  and  exact  local  alignments. BMC
       Bioinformatics, 12(Suppl 9):S15, 2011.