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. 2015 Feb 16;7(2):781–797. doi: 10.3390/v7020781

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© 2015 by the authors; licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).

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Sequence alignments before and after processing by the Automatic Alignment Clean-Up Tool (AACT). The sequence alignment, which was provided as input to the "AACT" tool (A) and the alignment produced by the tool (B). Columns containing at least 80% gaps (top, left of image) have been removed. Columns containing only one base type, with an ambiguous base, have been disambiguated (arrows). Columns containing a variety of bases are not altered. The alignments were visualized using the “JalView” program.