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jalviewApplet.jar and JmolApplet.jar

JalviewLite Button Examples

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Ferredoxins, chloroplast precursor related UniRef50 cluster

(15 sequences x 150 residues)

User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.
Displays a features file on the alignment
Associates PDB file 1GAQ with sequence FER1_MAIZE
Displays a Multiple Sequence Alignment Based JNet Prediction for a Sequence

RF00031 RFAM Alignment with per sequence secondary structure

Displays an RFAM RNA fold family with secondary structure annotation