Birte Kehr, David Weese, and Knut Reinert


Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast but heuristic, and hence often miss significant matches. We provide here the local pairwise aligner STELLAR that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy. STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments in the edit or hamming distance model.

STELLAR Binaries

Supported platforms are: Windows, Linux 64, and Mac OS X. Please take a look at the README file for usage instructions.

Version History

2012-11-28: v1.4

  • fixed: ArgumentParser value check
  • fixed: gapped X-drop extension for very high error penalties
  • fixed: comparison of overlapping eps-matches in special cases

2012-08-01: v1.3

  • conversion to new argument parser of SeqAn
  • added: option to select the alphabet type of input sequences

2012-04-20: v1.2

  • fixed: gff output mutations attribute
  • fixed: floating point problems on Windows, exponent padding
  • added: warning in case of non-unique fasta identifiers
  • small running time improvements

2011-09-17: v1.1

  • added: computation of E-values
  • added: print progress dots in verbosity mode
  • several small bug fixes
  • improvement of running time

2010-12-14: v1.0

  • first release of STELLAR Version 1.0



For questions, comments, or suggestions please contact Birte Kehr.

Last Update 28. November 2012