PDB structures may be displayed for Uniprot/Swiss-Prot protein sequences. Colours on the alignment, such as sequence features or conservation colouring can be visualised in the structure viewer.
Jmol 11.0.2 is used by Jalview 2.3

Jalview maintains the ability to perform Principal Component Analysis on an alignment. The method is used to cluster similar sequences, the user may then select sequences from this 3D visual display.

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