.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH KALIGN "1" "November 2022" "kalign 3.3.4" "User Commands"
.SH NAME
kalign \- Global and progressive multiple sequence alignment
.SH SYNOPSIS
.B kalign-avx2
\fI\,-i <seq file> -o <out aln>\/\fR
.SH DESCRIPTION
Kalign (3.3.4)
.SH OPTIONS
.TP
\fB\-\-format\fR
: Output format. [Fasta]
.TP
\fB\-\-type\fR
: Alignment type (rna, dna, internal). [rna]
Options: protein, divergent (protein)
.IP
rna, dna, internal (nuc).
.TP
\fB\-\-gpo\fR
: Gap open penalty. []
.TP
\fB\-\-gpe\fR
: Gap extension penalty. []
.TP
\fB\-\-tgpe\fR
: Terminal gap extension penalty. []
.TP
\fB\-n\fR/\-\-nthreads
: Number of threads. [4]
.TP
\fB\-\-version\fR (\fB\-V\fR/\-v)
: Prints version. [NA]
.SH EXAMPLES
Passing sequences via stdin:
.IP
cat input.fa | kalign \-f fasta > out.afa
.PP
Combining multiple input files:
.IP
kalign seqsA.fa seqsB.fa seqsC.fa \-f fasta > combined.afa
.SH COPYRIGHT
Copyright \(co 2006,2019,2020,2021 Timo Lassmann
.PP
This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign \fB\-showw\fR'.
.br
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.
.SS "Please cite:"
.IP
Lassmann, Timo.
"Kalign 3: multiple sequence alignment of large data sets."
Bioinformatics (2019)
https://doi.org/10.1093/bioinformatics/btz795