kalign 2.03-2 (lpia binary) in ubuntu intrepid

 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.