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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
.TH EDLIB-ALIGNER "1" "June 2018" "edlib-aligner 1.2.3" "User Commands"
.SH NAME
edlib-aligner \- edlib sequence alignment tool using edit distance
.SH SYNOPSIS
.B edlib-aligner
[\fI\,options\/\fR...] \fI\,<queries.fasta> <target.fasta>\/\fR
.SH OPTIONS
.TP
\fB\-s\fR
If specified, there will be no score or alignment output (silent mode).
.TP
\fB\-m\fR HW|NW|SHW
Alignment mode that will be used. [default: NW]
.TP
\fB\-n\fR 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]
.TP
\fB\-k\fR K
Sequences with score > K will be discarded. Smaller k, faster calculation. If \fB\-1\fR, no sequences will be discarded. [default: \fB\-1]\fR
.TP
\fB\-p\fR
If specified, alignment path will be found and printed. This may significantly slow down the calculation.
.TP
\fB\-l\fR
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.
.TP
\fB\-f\fR NICE|CIG_STD|CIG_EXT
Format that will be used to print alignment path, can be used only with \fB\-p\fR. NICE will give visually attractive format, CIG_STD will give standard cigar format and CIG_EXT will give extended cigar format. [default: NICE]
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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