tseemann / kalign

A fast multiple sequence alignment program.

Kalign

Kalign is a fast multiple sequence alignment program for biological sequences.

Install

git clone https://github.com/TimoLassmann/kalign.git 
cd kalign
./autogen.sh
make 
make check 
make install 

Usage

Usage: kalign  -i <seq file> -o <out aln> 

Options:

   --format           : Output format. [Fasta]
   --reformat         : Reformat existing alignment. [NA]

Kalign expects the input to be a set of unaligned sequences in fasta format or aligned sequences in aligned fasta, MSF or clustal format. Kalign automatically detects whether the input sequences are proten, RNA or DNA.

Examples

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Benchmark results

Here are some benchmark results. The code to reproduce these figures can be found here.

benchmark.org

Balibase

Bralibase

Homfam

Quantest2

Please cite:

Lassmann, Timo, Oliver Frings, and Erik LL Sonnhammer. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic acids research 37.3 (2008): 858-865.

Lassmann, Timo, and Erik LL Sonnhammer. Kalign–an accurate and fast multiple sequence alignment algorithm.

BMC bioinformatics 6.1 (2005): 298.