3 <head><title>Annotation Colouring</title></head>
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6 <p><strong> Annotation Colouring </strong></p>
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7 <p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based
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8 on any numerical annotation added to that alignment. </p>
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9 Select "Colour" <strong>→</strong> "..
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10 by Annotation" to bring up the Colour by Annotation settings window. <br>
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11 <br><div align="center">
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12 <img src="annotationColourSetting.jpg" width="426" height="140"> </div>
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14 <li>Select which annotation to base the colouring scheme on using the top left
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16 <li> If the "Use Original Colours" box is selected, the colouring
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17 scheme will use the colouring scheme present on the alignment before the Annotation
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18 Colour Settings window was displayed. </li>
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19 <li>The colour scheme can display a colour gradient from a colour representing
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20 the minimum value in the selected annotation to a colour representing the
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21 maximum value in the selected annotation. Use the "Min Colour" and
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22 "Max Colour" to set the colour gradient range.</li>
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23 <li>Select whether to colour the alignment above or below an adjustable threshold
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24 with the selection box center left of the window. </li>
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25 <li>Change the threshold value with the slider, or enter the exact value in
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28 <p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>
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