Project

AlignmentComparator - Visualizing differences between alternative multiple sequence alignments

Goal: AlignmentComparator is able to visually compare and annotate differences between alternative multiple sequence alignments (MSAs) of the same data set. 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. Manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm.

http://bioinfweb.info/AlignmentComparator/
https://github.com/bioinfweb/AlignmentComparator
http://twitter.com/bioinfweb
Legal notice: http://bioinfweb.info/AlignmentComparator/About
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Project log

Ben C Stöver
added an update
We switched to MantisBT as our bug tracking system, which is now open to all users. Check out http://bioinfweb.info/AlignmentComparator/Bugs if you want to report a bug a share a feature request with us.
 
Ben C Stöver
added an update
AlignmentComparator 1.1.0 is now available for download.
Changes:
  • 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.
 
Ben C Stöver
added an update
AlignmentComparator is now feature complete and left alpha state. Version 1.0.0 allows to compare any number of multiple sequence alignments and annotate the results in its GUI.
 
Ben C Stöver
added an update
AlignmentComparator 0.3.0 is now available for download. http://bioinfweb.info/AlignmentComparator/Download
Changes:
  • Open dialog now allows to filter files.
  • Labels for single compared alignment are now visible on every horizontal scroll position.
  • Bug fix: Superalignment along guide tree using the maximum sequence pair match algorithm now works correctly. (No alignment is shifted anymore.)
  • Bug fix: Single compared alignments do not move right anymore when zoomed out.
  • Bug fix: When opening a results file or starting a new comparison, the user is now asked to save the current comparison. (Fixes bug #178.)
  • Bug fix: Layout problems in dialog to start a comparison are fixed.
  • Bug fix: Duplicate empty namespace definitions are now avoided when saving a comparison to NeXML multiple times.
  • Bug fix: Correct height is now assigned to the components displaying single compared alignments, when a new comparison is performed or opened. (Fixes bug #177.)
 
Ben C Stöver
added an update
AlignmentComparator 0.2.0 is now available for download and allows to compare more than two alignments at a time with its maximum sequence pair match algorithm.
 
Ben C Stöver
added an update
AlignmentComparator 0.1.0 is now based on LibrAlign and JPhyloIO. It offers two new algorithms to comare alternative multiple sequence alignments of the same dataset and supports additional formats. Comparisons are now stored in NeXML.
 
Ben C Stöver
added an update
The AlignmentComparator source code repository now has a synchronized mirror on GitHub.
Feedback and pull requests are welcome.
 
Ben C Stöver
added 2 research items
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=100873
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. 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. Here we present AlignmentComparator, a platform independent open-source GUI application that reveals the differences and shifts in alternative MSAs by calculating and displaying a super alignment (similar to a profile-profile-alignment) that distinguishes between gaps previously contained in a single MSA and super gaps that originated from the comparison. This super alignment allows to directly identify matching regions in the alternative alignments, which otherwise would be very time-consuming with a conventional alignment editor, especially with an increasing column count and therefore a potentially increasing column shift. All differences can be commented and annotated with the AlignmentComparator GUI and saved to a XML file. Software and poster download: http://bioinfweb.info/AlignmentComparator http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=96833
Ben C Stöver
added a project goal
AlignmentComparator is able to visually compare and annotate differences between alternative multiple sequence alignments (MSAs) of the same data set. 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. Manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm.