NAME
gt-tirvish - Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.
SYNOPSIS
gt tirvish [option …] -index INDEXNAME
DESCRIPTION
- -index [string]
- 
specify the name of the enhanced suffix array index (mandatory) (default: undefined) 
- -seed [value]
- 
specify minimum seed length for exact repeats (default: 20) 
- -mintirlen [value]
- 
specify minimum length for each TIR (default: 100) 
- -maxtirlen [value]
- 
specify maximum length for each TIR (default: 1000) 
- -mintirdist [value]
- 
specify minimum distance of TIRs (default: 500) 
- -maxtirdist [value]
- 
specify maximum distance of TIRs (default: 10000) 
- -mat [value]
- 
specify matchscore for extension-alignment (default: 2) 
- -mis [value]
- 
specify mismatchscore for extension-alignment (default: -2) 
- -ins [value]
- 
specify insertionscore for extension-alignment (default: -3) 
- -del [value]
- 
specify deletionscore for extension-alignment (default: -3) 
- -xdrop [value]
- 
specify xdropbelowscore for extension-alignment (default: 5) 
- -similar [value]
- 
specify TIR similarity threshold in therange [1..100%] (default: 85.000000) 
- -overlaps […]
- 
specify no|best|longest|all (default: best) 
- -mintsd [value]
- 
specify minimum length for each TSD (default: 2) 
- -maxtsd [value]
- 
specify maximum length for each TSD (default: 11) 
- -vic [value]
- 
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) 
- -hmms
- 
profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format Omit this option to disable pHMM search. 
- -pdomevalcutoff [value]
- 
global E-value cutoff for pHMM search default 1E-6 
- -pdomcutoff […]
- 
model-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: GA) 
- -maxgaplen [value]
- 
maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50) 
- -refseqs [string]
- 
specify the name of the gene sequences to scan for inside candidates (default: undefined) 
- -seqids [yes|no]
- 
use sequence descriptions instead of sequence numbers in GFF3 output (default: yes) 
- -md5 [yes|no]
- 
add MD5 hashes to seqids in GFF3 output (default: no) 
- -help
- 
display help for basic options and exit 
- -help+
- 
display help for all options and exit 
- -version
- 
display version information and exit 
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.