Progressive alignment is a widely used approach to compute multiple sequence 
alignments (MSAs). However, aligning several hundred sequences by popular 
progressive alignment tools requires hours on sequential computers. Due to the 
rapid growth of sequence databases biologists have to compute MSAs in a far 
shorter time. In this paper we present a new approach to MSA on reconfigurable 
hardware platforms to gain high performance at low cost. We have constructed a 
linear systolic array to perform pairwise sequence distance computations using 
dynamic programming. This results in an implementation with significant runtime 
savings on a standard FPGA.