Aligning 415 519 proteins in less than two hours on PC

Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment algorithms. In the article we introduce FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilisation of longest common subsequence measure for determining pairwise similarities, a novel method of gap costs evaluation, and a new iterative refinement scheme. Importantly, its implementation is highly optimised and parallelised to make the most of modern computer platforms. Thanks to the above, quality indicators, namely sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms like Clustal Omega or MAFFT for datasets exceeding a few thousand of sequences. The quality does not compromise time and memory requirements which are an order of magnitude lower than that of existing solutions. For example, a family of 415 519 sequences was analysed in less than two hours and required only 8GB of RAM. FAMSA is freely available at http://sun.aei.polsl.pl/REFRESH/famsa.