The swift exact local aligner synopsis stellar [options] fasta file 1 fasta file 2 description 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 -h, --help displays this help message. --version display version information main options: -e, --epsilon num maximal error rate (max 0.25). in range [0.0000001..0.25]. default: 0.05. -l, --minlength num 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 str 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 num length of the q-grams (max 32). in range [1..32]. -rp, --repeatperiod num maximal period of low complexity repeats to be filtered. default: 1. -rl, --repeatlength num minimal length of low complexity repeats to be filtered. default: 1000. -c, --abundancecut num k-mer overabundance cut ratio. in range [0..1]. default: 1. verification options: -x, --xdrop num maximal x-drop for extension. default: 5. -vs, --verification str verification strategy: exact or bestlocal or bandedglobal one of exact, bestlocal, and bandedglobal. default: exact. -dt, --disablethresh num maximal number of verified matches before disabling verification for one query sequence (default infinity). in range [0..inf]. -n, --nummatches num maximal number of kept matches per query and database. if stellar finds more matches, only the longest ones are kept. default: 50. -s, --sortthresh num number of matches triggering removal of duplicates. choose a smaller value for saving space. default: 500. output options: -o, --out file name of output file. valid filetypes are: gff and txt. default: stellar.gff. -od, --outdisabled file name of output file for disabled query sequences. valid filetypes are: fa and fasta. default: stellar.disabled.fasta. references kehr, b., weese, d., reinert, k.: stellar: fast and exact local alignments. bmc bioinformatics, 12(suppl 9):s15, 2011. version stellar version: 1.3 last update october 2012