KALIGN

NAME

kalign - Global and progressive multiple sequence alignment

SYNOPSIS

kalign-avx2 -i <seq file> -o <out aln>

DESCRIPTION

Kalign (3.3.4)

OPTIONS

--format

: Output format. [Fasta]

--type

: Alignment type (rna, dna, internal). [rna] Options: protein, divergent (protein)

rna, dna, internal (nuc).

	--gpo		: Gap open penalty. []
	--gpe		: Gap extension penalty. []

--tgpe

: Terminal gap extension penalty. []

-n/--nthreads

: Number of threads. [4]

--version (-V/-v)

: Prints version. [NA]

EXAMPLES

Passing sequences via stdin:

cat input.fa | kalign -f fasta > out.afa

Combining multiple input files:

kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa

COPYRIGHT

Copyright © 2006,2019,2020,2021 Timo Lassmann

This program comes with ABSOLUTELY NO WARRANTY; for details type: ‘kalign -showw’.
This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details.

Please cite:

Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795