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| Class Summary | |
| AlignApplet | |
| AlignJFrame | Displays a grapical representation of a collection of sequences. | 
| ColourJFrame | Colour pallette display and editor. | 
| ColourMenu | Colour menu displayed in a popup menu from the colour display pallette (ColourJFrame). | 
| Consensus | Calculate a consensus using the same method as 'cons' in the EMBOSS suite. | 
| GraphicSequenceCollection | This class can be used to get a grapical representation of a collection of sequences. | 
| Matrix | |
| MatrixJFrame | |
| PatternJFrame | |
| PlotConsensus | |
| PrintAlignment | |
| PrintAlignmentImage | |
| Sequence | Sequence object | 
| SequenceJPanel | Applet for drawing sequence | 
| SequenceNameJButton | Draw sequence name | 
| SequenceProperties | |
| SequenceReader | This class reads sequences in FASTA and MSF format. | 
| SequenceSaver | This class saves sequences in FASTA format. | 
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