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MOTIVATION: Kalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. However, current alignment problems involving large numbers of sequences are exceeding Kalign's original design specifications. Here we present a completely re-written and updated version to meet current and future alignment challenges. RESULTS: Kalign now uses a SIMD accelerated version of the bit-parallel Gene Myers algorithm to estimate pariwise distances, adopts a sequence embedding strategy and the bi-secting K-means algorithm to rapidly construct guide trees for thousands of sequences. The new version maintains high alignment accuracy on both protein and nucleotide alignments and scales better than other MSA tools. AVAILABILITY: The source code of Kalign and code to reproduce the results are found here: https://github.com/timolassmann/kalign.
Timo Lassmann (Thu,) studied this question.