NAME

       sawriter - generate suffix arrays for nucleotide sequences

SYNOPSIS

       sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-larsson] [-4bit] [-manmy] [-kar]

       sawriter fastaIn  (writes to fastIn.sa).

OPTIONS

       -blt p      Build a lookup table on prefixes of length 'p'. This speeds

              up  lookups  considerably (more than the LCP table), but misses matches less than p
              when searching.

       -4bit  Read in (one) fasta file as a compressed sequence file.

       -larsson
              (default)  Uses the method of Larsson and Sadakane to build the array.

       -mamy  Uses the method of MAnber and MYers to build the array (slower than larsson,

              and produces the same result. This is mainly for double checking the correctness of
              larsson).

       -kark  Use  Karkkainen  DS3  method  for building the suffix array.  This will probably be
              more slow than larsson, but takes only an extra N/(sqrt 3) extra space.

       -mafe  (disabled for now!) Use the lightweight construction  algorithm  from  Manzini  and
              Ferragina

       -welter
              Use lightweight (sort of light) suffix array construction.  This is a bit more slow
              than normal larsson.

       -welterweight N use a difference cover of size N for building the suffix array.
              Valid values are 7,32,64,111, and 2281.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.