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stellar - the SwifT Exact LocaL AligneR




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.


Display the help message.
Display version information.

Main Options:

Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.
Minimal length of epsilon-matches. In range [0..inf]. Default: 100.
Search only in forward strand of database.
Search only in reverse complement of database.
Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of dna, dna5, rna, rna5, protein, and char.
Set verbosity mode.

Filtering Options:

Length of the q-grams (max 32). In range [1..32].
Maximal period of low complexity repeats to be filtered. Default: 1.
Minimal length of low complexity repeats to be filtered. Default: 1000.
k-mer overabundance cut ratio. In range [0..1]. Default: 1.

Verification Options:

Maximal x-drop for extension. Default: 5.
Verification strategy: exact or bestLocal or bandedGlobal One of exact, bestLocal, and bandedGlobal. Default: exact.
Maximal number of verified matches before disabling verification for one query sequence (default infinity). In range [0..inf].
Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept. Default: 50.
Number of matches triggering removal of duplicates. Choose a smaller value for saving space. Default: 500.

Output Options:

Name of output file. Valid filetypes are: .txt and .gff. Default: stellar.gff.
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.

stellar 1.4.11 [tarball]