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There are various coloring schemes for DNA and amino alphabets available.

To change the scheme, activate the Colors context menu:

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     <img src="/wiki/download/attachments/4227448/Coloring Schemes.png"/>
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</center>

or use the Highlighting tab of the Options Panel:

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     <img src="/wiki/download/attachments/4227448/Coloring Schemes_1.png"/>
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</center>