kalign binary package in Ubuntu Trusty i386

 Kalign is a command line tool to perform multiple alignment of
 biological sequences. It employs the Muth-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.

Source package