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 © 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