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-<head>
-<title>Colour Schemes</title>
-<style type="text/css">
-<!--
-td {
- font-family: "Courier New", Courier, mono;
- font-style: normal;
- font-size: medium;
-}
--->
-</style>
-</head>
-<body>
- <p>
- <strong>Colour schemes</strong>
- </p>
- <p>Jalview allows the user to set a colour scheme for the
- whole alignment view or for each group defined on regions within it.</p>
- <p>To change the colour for a view, simply select a new colour scheme from
- the "Colour" menu.</p>
- <p>To change the colour of a group, right click on any residue
- within a group and use the popup menu to define the group colour.</p>
- <p>At the top of the "Colour" menu you'll see a tick box
- "Apply Colour to all groups". This is ticked by
- default so that a chosen colour scheme will be applied to all
- existing groups. If you wish to maintain the colour scheme for
- defined groups, make sure you deselect this option before selecting
- a new scheme in the Colour menu.</p>
- <p>
- The <strong>"Colour→<a
- href="../colourSchemes/textcolour.html">Colour Text...</a>"
- </strong> entry opens a dialog box to set a different text colour for light
- and dark background, and the intensity threshold for transition
- between them.
- </p>
- <p>The default colour schemes are summarised in the table below:
- <div align="center">
- <p> </p>
- <p>
- <strong>Protein Colour Schemes</strong>
- </p>
- <table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td>
- <td>R</td>
- <td>N</td>
- <td>D</td>
- <td>C</td>
- <td>Q</td>
- <td>E</td>
- <td>G</td>
- <td>H</td>
- <td>I</td>
- <td>L</td>
- <td>K</td>
- <td>M</td>
- <td>F</td>
- <td>P</td>
- <td>S</td>
- <td>T</td>
- <td>W</td>
- <td>Y</td>
- <td>V</td>
- <td>B</td>
- <td>X</td>
- <td>Z</td>
- </tr>
- <tr>
- <td height="24">Clustal</td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f08080"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f09048"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Zappo</td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffafaf"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Taylor</td>
- <td bgcolor="#ccff00"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#cc00ff"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#ff00cc"></td>
- <td bgcolor="#ff0066"></td>
- <td bgcolor="#ff9900"></td>
- <td bgcolor="#0066ff"></td>
- <td bgcolor="#66ff00"></td>
- <td bgcolor="#33ff00"></td>
- <td bgcolor="#6600ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff66"></td>
- <td bgcolor="#ffcc00"></td>
- <td bgcolor="#ff3300"></td>
- <td bgcolor="#ff6600"></td>
- <td bgcolor="#00ccff"></td>
- <td bgcolor="#00ffcc"></td>
- <td bgcolor="#99ff00"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Hydrophobicity</td>
- <td bgcolor="#ad0052"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#c2003d"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#6a0095"></td>
- <td bgcolor="#1500ea"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ea0015"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#b0004f"></td>
- <td bgcolor="#cb0034"></td>
- <td bgcolor="#4600b9"></td>
- <td bgcolor="#5e00a1"></td>
- <td bgcolor="#61009e"></td>
- <td bgcolor="#5b00a4"></td>
- <td bgcolor="#4f00b0"></td>
- <td bgcolor="#f60009"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#680097"></td>
- <td bgcolor="#0c00f3"></td>
- </tr>
- <tr>
- <td>Helix Propensity</td>
- <td bgcolor="#e718e7"></td>
- <td bgcolor="#6f906f"></td>
- <td bgcolor="#1be41b"></td>
- <td bgcolor="#778877"></td>
- <td bgcolor="#23dc23"></td>
- <td bgcolor="#926d92"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#ae51ae"></td>
- <td bgcolor="#a05fa0"></td>
- <td bgcolor="#ef10ef"></td>
- <td bgcolor="#986798"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#36c936"></td>
- <td bgcolor="#47b847"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#21de21"></td>
- <td bgcolor="#857a85"></td>
- <td bgcolor="#49b649"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#c936c9"></td>
- </tr>
- <tr>
- <td nowrap>Strand Propensity</td>
- <td bgcolor="#5858a7"></td>
- <td bgcolor="#6b6b94"></td>
- <td bgcolor="#64649b"></td>
- <td bgcolor="#2121de"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#8c8c73"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#60609f"></td>
- <td bgcolor="#ecec13"></td>
- <td bgcolor="#b2b24d"></td>
- <td bgcolor="#4747b8"></td>
- <td bgcolor="#82827d"></td>
- <td bgcolor="#c2c23d"></td>
- <td bgcolor="#2323dc"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#c0c03f"></td>
- <td bgcolor="#d3d32c"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#4343bc"></td>
- <td bgcolor="#797986"></td>
- <td bgcolor="#4747b8"></td>
- </tr>
- <tr>
- <td>Turn Propensity</td>
- <td bgcolor="#2cd3d3"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#e81717"></td>
- <td bgcolor="#a85757"></td>
- <td bgcolor="#3fc0c0"></td>
- <td bgcolor="#778888"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#00ffff"></td>
- <td bgcolor="#1ce3e3"></td>
- <td bgcolor="#7e8181"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#f60909"></td>
- <td bgcolor="#e11e1e"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#9d6262"></td>
- <td bgcolor="#07f8f8"></td>
- <td bgcolor="#f30c0c"></td>
- <td bgcolor="#7c8383"></td>
- <td bgcolor="#5ba4a4"></td>
- </tr>
- <tr>
- <td>Buried Index</td>
- <td bgcolor="#00a35c"></td>
- <td bgcolor="#00fc03"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#009d62"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#0054ab"></td>
- <td bgcolor="#007b84"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#009768"></td>
- <td bgcolor="#008778"></td>
- <td bgcolor="#00e01f"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#00db24"></td>
- <td bgcolor="#00a857"></td>
- <td bgcolor="#00e619"></td>
- <td bgcolor="#005fa0"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00b649"></td>
- <td bgcolor="#00f10e"></td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- <p> </p>
- <p>
- <strong>Nucleotide Colour Schemes</strong>
- </p>
- <table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td>
- <!--Adenine-->
- <td>C</td>
- <!--Cytosine-->
- <td>G</td>
- <!--Guanine-->
- <td>T</td>
- <!--Thymine-->
- <td>U</td>
- <!--Uracil-->
- <td>I</td>
- <!--Inosine-->
- <td>X</td>
- <!--Xanthine-->
- <td>R</td>
- <!--Unknown Purine-->
- <td>Y</td>
- <!--Unknown Pyrimidine-->
- <td>N</td>
- <!--Unknown-->
- <td>W</td>
- <!--Weak nucleotide (A or T)-->
- <td>S</td>
- <!--Strong nucleotide (G or C)-->
- <td>M</td>
- <!--Amino (A or C)-->
- <td>K</td>
- <!--Keto (G or T)-->
- <td>B</td>
- <!--Not A (G or C or T)-->
- <td>H</td>
- <!--Not G (A or C or T)-->
- <td>D</td>
- <!--Not C (A or G or T)-->
- <td>V</td>
- <!--Not T (A or G or C-->
- </tr>
- <tr>
- <td height="24">Nucleotide</td>
- <td bgcolor="#64F73F"></td>
- <td bgcolor="#FFB340"></td>
- <td bgcolor="#EB413C"></td>
- <td bgcolor="#3C88EE"></td>
- <td bgcolor="#3C88EE"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Purine/Pyrimidine</td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
-
-
- </div>
- <p align="center"> </p>
-</body>
-</html>