specify the name of the enhanced suffix array index (mandatory) (default: undefined)

specify minimum seed length for exact repeats (default: 20)

specify minimum length for each TIR (default: 100)

specify maximum length for each TIR (default: 1000)

specify minimum distance of TIRs (default: 500)

specify maximum distance of TIRs (default: 10000)

specify matchscore for extension-alignment (default: 2)

specify mismatchscore for extension-alignment (default: -2)

specify insertionscore for extension-alignment (default: -3)

specify deletionscore for extension-alignment (default: -3)

specify xdropbelowscore for extension-alignment (default: 5)

specify TIR similarity threshold in therange [1..100%] (default: 85.000000)

specify no|best|longest|all (default: best)

specify minimum length for each TSD (default: 2)

specify maximum length for each TSD (default: 11)

specify the number of nucleotides (to the left and to the right) that will be searched for TSDs around 5' and 3' boundary of predicted TIRs (default: 60)

profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format Omit this option to disable pHMM search.

global E-value cutoff for pHMM search default 1E-6

model-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: GA)

maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)

specify the name of the gene sequences to scan for inside candidates (default: undefined)

use sequence descriptions instead of sequence numbers in GFF3 output (default: yes)

add MD5 hashes to seqids in GFF3 output (default: no)

display help for basic options and exit

display help for all options and exit

display version information and exit