Download the latest version of AlignmentComparator

This is the latest version of AlignmentComparator (0.1.0-193 alpha) which was released on 2018-02-13 20:25:00.0.


GNU General Public License, version 3

AlignmentComparator is distributed under GNU General Public License. Copyright (C) 2012-2017 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

  • Maximum sequence pair match comparison algorithm added.
  • Average index comparison algorithm added, which can also compare more than two alignments at the same time.
  • GUI components are now based on LibrAlign.
  • Each compared alignment now has its own scroll container.
  • NeXML now used to store comparison results.
  • I/O is now based on JPhyloIO which allows to read FASTA, Phylip, Nexus and NeXML.
  • Functionality to add comments and manually edit the superalignment is currently not available.

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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