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kalign Documentation


Global and progressive multiple sequence alignment
Kalign is a command line tool to perform multiple alignment of
biological sequences. It employs the Wu-Manber string-matching
algorithm, to improve both the accuracy and speed of the alignment.
It uses global, progressive alignment approach, enriched by employing
an approximate string-matching algorithm to calculate sequence
distances and by incorporating local matches into the otherwise global
alignment. In comparisons made by its authors, Kalign was about 10
times faster than ClustalW and, depending on the alignment size, up to
50 times faster than popular iterative methods. It has been published
in Lassmann and Sonnhammer, BMC Bioinformatics 2005, 6:298.
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