  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.
