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[](https://github.com/TimoLassmann/kalign/actions/workflows/cmake.yml)
[](https://github.com/TimoLassmann/kalign/actions/workflows/python.yml)
[](https://github.com/TimoLassmann/kalign/actions/workflows/wheels.yml)
# Kalign
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.
## Installation
### From source
Prerequisites: C compiler (GCC or Clang), CMake 3.18+, optionally OpenMP.
```bash
mkdir build && cd build
cmake ..
make
make test
make install
```
On macOS, `brew install libomp` for OpenMP support.
### Zig build (alternative)
Requires zig version 0.12.
```bash
zig build
```
### Python
```bash
pip install kalign-python
```
See [README-python.md](README-python.md) for the full Python documentation.
## Usage
```
kalign -i <input> -o <output>
```
Kalign v3.5 has three modes:
| Mode | Flag | Description |
|------|------|-------------|
| default | (none) | Best general-purpose. |
| fast | `--fast` | Fastest. Same as kalign v3.4. |
| precise | `--precise` | Highest accuracy, ~10x slower. |
### Examples
```bash
# Align sequences
kalign -i sequences.fa -o aligned.fa
# Fast mode
kalign --fast -i sequences.fa -o aligned.fa
# Precise mode (ensemble + realign)
kalign --precise -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
# Save ensemble consensus for re-thresholding
kalign --precise -i seqs.fa -o out.fa --save-poar consensus.poar
kalign -i seqs.fa -o out2.fa --load-poar consensus.poar --min-support 3
```
### Options
```
--format Output format: fasta, msf, clu. [fasta]
--type Sequence type: protein, dna, rna, divergent. [auto]
--gpo Gap open penalty. [auto]
--gpe Gap extension penalty. [auto]
--tgpe Terminal gap extension penalty. [auto]
--ensemble N Run N ensemble alignments. [off]
--refine Refinement: none, all, confident. [none]
-n Number of threads. [auto]
```
### Output formats
```bash
kalign -i input.fa -f msf -o output.msf
kalign -i input.fa -f clu -o output.clu
```
## C library
Link Kalign into your C/C++ project:
```cmake
find_package(kalign)
target_link_libraries(<target> kalign::kalign)
```
Or include directly:
```cmake
add_subdirectory(<path>/kalign EXCLUDE_FROM_ALL)
target_link_libraries(<target> kalign::kalign)
```
## Benchmarks
### Balibase
### Bralibase
## Citation
Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets."
Bioinformatics (2019). [DOI](https://doi.org/10.1093/bioinformatics/btz795)
## License
Apache License, Version 2.0. See [COPYING](COPYING).
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