edlib-aligner - edlib sequence alignment tool using edit
distance
edlib-aligner [options...] <queries.fasta>
<target.fasta>
- -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]
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.