prefix for output files (e.g. foo will create files called foo_*.csv and foo_*.fas) Omit this option for GFF3 output only.

output metadata (run conditions) to separate file (default: yes)

set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)

required PPT length range (default: [8..30])

required U-box length range (default: [3..30])

allowed U-box distance range from PPT (default: 0)

radius around beginning of 3' LTR to search for PPT (default: 30)

purine emission probability inside PPT (default: 0.970000)

pyrimidine emission probability inside PPT (default: 0.030000)

background G emission probability outside PPT (default: 0.250000)

background C emission probability outside PPT (default: 0.250000)

background A emission probability outside PPT (default: 0.250000)

background T emission probability outside PPT (default: 0.250000)

U/T emission probability inside U-box (default: 0.910000)

tRNA library in multiple FASTA format for PBS detection Omit this option to disable PBS search.

required PBS/tRNA alignment length range (default: [11..30])

allowed PBS offset from LTR boundary range (default: [0..5])

allowed PBS/tRNA 3' end alignment offset range (default: [0..5])

maximal allowed PBS/tRNA alignment unit edit distance (default: 1)

radius around end of 5' LTR to search for PBS (default: 30)

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: NONE)

output pHMM to amino acid sequence alignments (default: no)

output amino acid sequences for protein domain hits (default: no)

output features from all chains and unchained features, labeled with chain numbers (default: no)

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

force recreation of hmmpressed profiles (default: no)

match score for PBS/tRNA alignments (default: 5)

mismatch score for PBS/tRNA alignments (default: -10)

insertion score for PBS/tRNA alignments (default: -20)

deletion score for PBS/tRNA alignments (default: -20)

be verbose (default: no)

redirect output to specified file (default: undefined)

write gzip compressed output file (default: no)

write bzip2 compressed output file (default: no)

force writing to output file (default: no)

set the sequence file from which to take the sequences (default: undefined)

set the encoded sequence indexname from which to take the sequences (default: undefined)

set the sequence files from which to extract the features use -- to terminate the list of sequence files

search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)

exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)

use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001) (default: no)

set file containing sequence-region to sequence file mapping (default: undefined)

display help for basic options and exit

display help for all options and exit

display version information and exit