mkESA: enhanced suffix array construction tool. Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data. Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at

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  1. Ohlebusch, Enno; Beller, Timo; Abouelhoda, Mohamed I.: Computing the Burrows-Wheeler transform of a string and its reverse in parallel (2014)
  2. Homann, Robert; Fleer, David; Giegerich, Robert; Rehmsmeier, Marc: \textitmkesa: enhanced suffix array construction tool (2009) ioport