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Many new features have been added to the Jalview interface, such as
the Overview window which aids navigation around the whole alignment.
Search using regular expressions.
The functionality of the original Jalview has been maintained and enhanced
in the new interface. Below is an example of an average distance tree,
calculated from the input alignment, being used to cluster sequences in
the main alignment window.
The user has then applied "Conservation Colouring" to the alignment,
the result of which shows conservation within the clustered sequences.
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