kalign1
Global and progressive multiple sequence alignment
Usage
kalign-avx2 -i
<seq
file>
-o
<out
aln>
Overview
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
Releases
10 releases since Debian 4.0 (Etch); the text changed 4 times.
--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).