A system for aligning nucleotide or amino acid biosequences is described. The system, called
Neweyes, employs a novel string matching algorithm, Running Karp-Rabin Greedy String Tiling
(RKR-GST), which involves tiling one string with matching substrings of a second string. In
practice, RKR-GST has a computational complexity that appears close to linear. With RKR-GST,
Neweyes is able to detect transposed substrings. Neweyes also supports a form of matching-bygroup
that gives the effect of different amino acid mutation matrices. Neweyes can be used in a
macro mode (searching a database for a list of biosequences that are similar to a given
biosequence) or in a micro mode, where two biosequences are compared and more detailed output
formats are available.