NAME

       edlib-aligner - edlib sequence alignment tool using edit distance

SYNOPSIS

       edlib-aligner [options...] <queries.fasta> <target.fasta>

OPTIONS

       -s     If specified, there will be no score or alignment output (silent mode).

       -m HW|NW|SHW
              Alignment mode that will be used. [default: NW]

       -n N   Score will be calculated only for N best sequences (best = with smallest score). If
              N = 0 then all sequences will be calculated. Specifying  small  N  can  make  total
              calculation much faster. [default: 0]

       -k K   Sequences  with  score > K will be discarded. Smaller k, faster calculation. If -1,
              no sequences will be discarded. [default: -1]

       -p     If specified, alignment path will be found and printed. This may significantly slow
              down the calculation.

       -l     If  specified,  start  locations  will  be  found  and printed. Each start location
              corresponds to one end location. This may somewhat slow down the  calculation,  but
              is still faster then finding alignment path and does not consume any extra memory.

       -f NICE|CIG_STD|CIG_EXT
              Format  that  will  be used to print alignment path, can be used only with -p. NICE
              will give visually attractive format, CIG_STD will  give standard cigar format  and
              CIG_EXT will give extended cigar format. [default: NICE]

AUTHOR

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