GT-LTRHARVEST(1)

NAME
gt-ltrharvest - Predict LTR retrotransposons.

SYNOPSIS

gt ltrharvest [option ...] -index <indexname>

OPTIONS

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

-range
    specify range in the input sequence(s) in which LTR pairs are searched (default: 0 0)

-seed
    specify minimum seed length for exact repeats (default: 30)

-minlenltr
    specify minimum length for each LTR (default: 100)

-maxlenltr
    specify maximum length for each LTR (default: 1000)

-mindistltr
    specify minimum distance of LTR startpositions (default: 1000)

-maxdistltr
    specify maximum distance of LTR startpositions (default: 15000)

-similar
    specify similaritythreshold in range [1..100%] (default: 85.00)

-mintsd
    specify minimum length for each TSD (default: 4)

-maxtsd
    specify maximum length for each TSD (default: 20)

-motif
    specify 2 nucleotides startmotif + 2 nucleotides endmotif: ** (default: undefined)

-motifmis
    specify maximum number of mismatches in motif [0,3] (default: 4)

-vic
    specify the number of nucleotides (to the left and to the right) that will be searched for TSDs and/or motifs around 5' and 3' boundary of predicted LTR retrotransposons (default: 60)

-overlaps
    specify no|best|all (default: best)

-xdrop
    specify xdropbelowscore for extension-alignment (default: 5)

-mat
    specify matchscore for extension-alignment (default: 2)

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

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

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

-v
    verbose mode (default: no)

-longoutput
    additional motif/TSD output (default: no)

-out
    specify FASTA outputfilename (default: undefined)

-outinner
    specify FASTA outputfilename for inner regions (default: undefined)

-gff3
    specify GFF3 outputfilename (default: undefined)

-help
    display help for basic options and exit

-help+
    display help for all options and exit

-version
    display version information and exit

DESCRIPTION

For detailed information, please refer to the manual of ltrharvest.

AUTHOR

Report bugs to <gt-users@genometools.org>.