Download the latest version of AlignmentComparator

This is the latest version of AlignmentComparator (1.1.0-299 beta) which was released on 2018-04-18 18:20:00.0.


GNU General Public License, version 3

AlignmentComparator is distributed under GNU General Public License. Copyright (C) 2012-2018 by Ben Stöver. This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

By downloading AlignmentComparator you agree with the License. Please read it carefully.


Complete download

The complete download contains the classes of all components associated with this release.

Binary release (all platforms) Download icon AlignmentComparator

[Browse source codes]


Developers can also check out the source codes directly from the subversion repository under

Changes in this version

  • Average unaligned position approach improved by calculating relative positions within gaps and selecting column merge sides depending in future merges.
  • Average columns positions are now shown again in the GUI when using this comparison approach.
  • Average unaligned position approach now uses absolute instead of relative sequence positions. (As a result all regions are now always superaligned equally, no matter which sequence patterns are found in front of them.)
  • Corresponding positions in other MSAs are now highlighted when selecting columns in one MSA.
  • Amino acid color schema is now available.
  • Bug fix: Action status is now refreshed when the comment selection is changed.
  • Further bug fixes.

Previous versions

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AlignmentComparator poster IPAM MSA Workshop 2015 Conference poster at IPAM MSA Workshop in Jan 2015

AlignmentComparator poster at MSGE Symposium 2014 Conference poster at MSGE Symposium in June 2014

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