mkESA is an open source program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on our implementation of Manzini's lightweight Deep-Shallow algorithm [1], which can also utilize multiple CPUs/cores for some extra speed-up. The generated output is compatible with the output of mkvtree from the Vmatch package written by Stefan Kurtz.

mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 or higher. Try our download page.