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

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 is distributed under GNU General Public License version 3.

Features

Graphically compare two alternative alignments of the same data set.
Supports FASTA, Phylip, Nexus and NeXML.
Stores comparison results in NeXML.

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.