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>.

                                            10/07/2012                           GT-LTRHARVEST(1)