NAME

       gt-ltrharvest - Predict LTR retrotransposons.

SYNOPSIS

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

DESCRIPTION

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

       -range [start end]
           specify range in the input sequence(s) in which LTR pairs are searched (default:
           [0..0])

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

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

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

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

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

       -similar [value]
           specify similaritythreshold in range [1..100%] (default: 85.000000)

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

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

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

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

       -vic [value]
           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 [value]
           specify xdropbelowscore for extension-alignment (default: 5)

       -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)

       -v [yes|no]
           verbose mode (default: no)

       -tabout [yes|no]
           show old tabular output instead of GFF3 on stdout (default: yes)

       -seqids [yes|no]
           use sequence descriptions instead of sequence numbers in GFF3 output (default: no)

       -md5 [yes|no]
           add MD5 hashes to seqids in GFF3 output (default: no)

       -longoutput [yes|no]
           additional motif/TSD output (default: no)

       -out [string]
           specify FASTA outputfilename (default: undefined)

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

       -gff3 [string]
           specify GFF3 outputfilename (default: undefined)

       -offset [value]
           offset added to GFF3 coordinates (default: 0)

       -scan [yes|no]
           scan the index sequentially instead of mapping it into memory entirely (default: yes)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

ADDITIONAL INFORMATION

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

REPORTING BUGS

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