BioInfWeb - AlignmentComparator

AlignmentComparator - An application to efficiently visualize and annotate differences between alternative multiple sequence alignments

Screenshot of AlignmentComparator
Example of a comparison of two alternative alignments with AlignmentComparator

With a growing number of alternative algorithms for automated multiple sequence alignment (MSA) and different strategies for manual alignment corrections it becomes more and more relevant to visualize the differences between alternative MSAs of the same data set. AlignmentComparator is a desktop application that visualizes the differences between two alternative alignments of the same data set and allows to annotate and comment them. This allows the researcher to decide which alternative alignments to take into account as the bases of e.g. a phylogenetic study or numerous other tasks in biological research. Furthermore, manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm, which both is very relevant in our current research focusing on the improvement of MSA for phylogenetic purposes.

AlignmentComparator is currently in alpha stage and is distributed under GNU General Public License version 3. Later releases will be available on this website.


  • Graphically compare two FASTA files containing alternative alignments of the same data set. (More alignment formats will be supported in later versions.)
  • Manually change the comparison if needed
  • Annotate and comment the differences
  • Save your results to an XML file

Further information

A detailed documentation of the usage of AlignmentComparator will be provided in this website before AlignmentComparator reaches beta stage. Until than you can find further information on this conference poster.

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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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