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.

edlib-aligner 1.2.3                                 June 2018                                   EDLIB-ALIGNER(1)