Kalign is a fast multiple sequence alignment program for biological sequences. It aligns protein, DNA, and RNA sequences using a progressive alignment approach with multi-threading support.

Prerequisites: C compiler (GCC or Clang), CMake 3.18+.

mkdir build && cd build
cmake ..
make
make test
make install

Kalign uses a built-in thread pool for parallelization (requires pthreads, available on all POSIX systems). If pthreads is not available, it falls back to serial execution. To use OpenMP instead:

cmake -DUSE_OPENMP=ON -DUSE_THREADPOOL=OFF ..

Requires zig version 0.12.

zig build

pip install kalign-python

See README-python.md for the full Python documentation.

kalign -i <input> -o <output>

Kalign has four mode presets, optimized for protein and nucleotide sequences:

# Align sequences (default mode)
kalign -i sequences.fa -o aligned.fa

# Fast mode
kalign --mode fast -i sequences.fa -o aligned.fa

# Accurate mode (ensemble)
kalign --mode accurate -i sequences.fa -o aligned.fa

# Read from stdin
cat input.fa | kalign -i - -o aligned.fa

# Combine multiple input files
kalign seqsA.fa seqsB.fa -o combined.fa

--mode         Mode preset: fast, default, recall, accurate. [default]
--format       Output format: fasta, msf, clu. [fasta]
--type         Sequence type: protein, dna, rna, divergent. [auto]
--gpo          Gap open penalty (overrides preset). [auto]
--gpe          Gap extension penalty (overrides preset). [auto]
--tgpe         Terminal gap extension penalty (overrides preset). [auto]
-n             Number of threads. [auto]

kalign -i input.fa -f msf -o output.msf
kalign -i input.fa -f clu -o output.clu

Link Kalign into your C/C++ project:

find_package(kalign)
target_link_libraries(<target> kalign::kalign)

Or include directly:

add_subdirectory(<path>/kalign EXCLUDE_FROM_ALL)
target_link_libraries(<target> kalign::kalign)

Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019). DOI

Apache License, Version 2.0. See COPYING.