Help -hshow usage and the full list of flags
Lossy seeds -spaced -w 11,11 -s 11,18 -l 64search the best spaced seed of weight 11, span ≤ 18, on alignments of length 64 -spaced -w 11,11 -s 11,22 -l 64 -n 2 -r 10000 -ksearch a good pair of spaced seeds (weight 11, span ≤ 22) : 10000 trials with hillclimbing -transitive -w 11,11 -s 13,18 -l 64 -r 10000 -ksearch a good transitive seed, weight 11, span between 13 and 18 : 10000 trials with hillclimbing -iupac -s 12,16 -l 64 -m RYNNNNNNNNNN -i shuffle -r 5000 -k -z 500search a good IUPAC seed from the pattern by shuffling it : 5000 trials with hillclimbing, state report every 500 -A 2 -B 3 -f 0.3,0.7 -M {{1,1},{1,1},{0,1}} -V -S {{0,0},{0,1},{0,0}} -BSymbols '-x#' -s 14,24 -i 0,4,10 -T 3 -r 10000 -ksearch a good seed where ≤ 1 mismatch is allowed on 'x' symbols
Lossless seeds -spaced -w 12,12 -s 19,19 -l 25 -L 1,0 -X 2search a lossless spaced seed (weight 12, span 19) on alignments of length 25 with 2 mismatches -spaced -w 14,14 -s 20,21 -l 25 -L 1,0 -X 2 -n 2 -m ####-#-##--####-#-##,#-##--####-#-##--####test if the pair of seeds is lossless on alignments of length 25 with 2 mismatches
files
Some flags (-fF, -pF, -SF, -MF, -e, -o, ...) take a file argument. Add files here,
then reference the exact "virtual name" shown below in your command line.
Files written by a run (e.g. via -o) appear here too — reuse the same
virtual name for -e and -o to iterate: press Up, Enter again to keep improving.