kalign(1)

Global and progressive multiple sequence alignment

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

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

History

Debian 13 (Trixie) to Debian 12 (Bookworm): the text shown here
Debian 11 (Bullseye)
Debian 10 (Buster) to Debian 6.0 (Squeeze)
Debian 5.0 (Lenny)
Debian 4.0 (Etch)

--format since Debian 11 (Bullseye); --gpe since Debian 12 (Bookworm); --gpo since Debian 12 (Bookworm); --tgpe since Debian 12 (Bookworm); --type since Debian 12 (Bookworm); --version since Debian 11 (Bullseye).

--reformat until Debian 11 (Bullseye); -a until Debian 10 (Buster); -bonus until Debian 10 (Buster); -diff_feature_score until Debian 10 (Buster); -e until Debian 10 (Buster); -f until Debian 4.0 (Etch); -fast until Debian 4.0 (Etch); -feature until Debian 10 (Buster); -g until Debian 10 (Buster); -gap_ext until Debian 10 (Buster); -gap_inc until Debian 10 (Buster); -gap_open until Debian 10 (Buster); -gapextension until Debian 10 (Buster); -gapopen until Debian 10 (Buster); -gpe until Debian 10 (Buster); -gpo until Debian 10 (Buster); -i until Debian 10 (Buster); -in until Debian 10 (Buster); -input until Debian 10 (Buster); -m until Debian 10 (Buster); -matrix_bonus until Debian 10 (Buster); -o until Debian 10 (Buster); -out until Debian 10 (Buster); -output until Debian 10 (Buster); -p until Debian 4.0 (Etch); -points until Debian 4.0 (Etch); -q until Debian 10 (Buster); -quiet until Debian 10 (Buster); -s until Debian 10 (Buster); -same_feature_score until Debian 10 (Buster); -t until Debian 10 (Buster); -terminal_gap_extension_penalty until Debian 10 (Buster); -tgpe until Debian 10 (Buster); -w until Debian 4.0 (Etch); -z until Debian 10 (Buster); -zcutoff until Debian 10 (Buster).