Man page - gt-tirvish(1)
Packages contains this manual
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- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
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- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
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- gt-compreads-refcompress(1)
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- gt-clean(1)
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- gt-seq(1)
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- gt-sequniq(1)
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- gt-gtf_to_gff3(1)
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- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
- gt-uniquesub(1)
- gt-encseq-sample(1)
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- gt-compreads-compress(1)
- gt-scriptfilter(1)
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- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
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- gt-encseq-check(1)
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- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
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- gt-interfeat(1)
apt-get install genometools
Manual
GT-TIRVISH
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
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.