Provided by: genometools_1.5.1-2ubuntu1_amd64 bug


       gt-suffixerator - Compute enhanced suffix array.


       gt suffixerator [option ...] (-db file [...] | -ii index)


           output sequence separator positions to file (default: yes)

           output sequence descriptions to file (default: yes)

           output sequence description separator positions to file (default: yes)

           output MD5 sums to file (default: yes)

           specify kind of sequence representation by one of the keywords direct, bytecompress,
           eqlen, bit, uchar, ushort, uint32 (default: undefined)

           input is DNA sequence (default: no)

           input is protein sequence (default: no)

           specify name for index to be generated (default: undefined)

           specify database files

           specify file containing a symbol mapping (default: undefined)

           allow lossless original sequence retrieval (default: no)

           virtually append the reverse complement of each sequence (default: no)

           specify prefix length for bucket sort recommendation: use without argument; then a
           reasonable prefix length is automatically determined. (default: 0)

           specify difference cover value (default: 0)

           optimize esa-construction for suffix-prefix matching (default: 0)

           specify maximal amount of memory to be used during index construction (in bytes, the
           keywords MB and GB are allowed) (default: undefined)

           output/sort according to keys of the form |key| in fasta header (default: nosort)

           specify reading direction (fwd, cpl, rev, rcl) (default: fwd)

           output suffix array (suftab) to file (default: no)

           output lcp table (lcptab) to file (default: no)

           output Burrows-Wheeler Transformation (bwttab) to file (default: no)

           output bucket table to file (default: no)

           be verbose (default: no)

           show a progress bar (default: no)

           specify existing encoded sequence (default: undefined)

           display help for basic options and exit

           display help for all options and exit

           display version information and exit


       Report bugs to <>.

                                            10/07/2012                         GT-SUFFIXERATOR(1)