<mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
<mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
<mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
+ <mapID target="colours.gecos-flower" url="html/colourSchemes/gecos-flower.html" />
+ <mapID target="colours.gecos-blossom" url="html/colourSchemes/gecos-blossom.html" />
+ <mapID target="colours.gecos-sunset" url="html/colourSchemes/gecos-sunset.html" />
+ <mapID target="colours.gecos-ocean" url="html/colourSchemes/gecos-ocean.html" />
<mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
<mapID target="colours.helix" url="html/colourSchemes/helix.html" />
<mapID target="colours.strand" url="html/colourSchemes/strand.html" />
<tocitem text="ClustalX" target="colours.clustal" />
<tocitem text="Zappo" target="colours.zappo" />
<tocitem text="Taylor" target="colours.taylor" />
+ <tocitem text="gecos:flower" target="colours.gecos-flower" />
+ <tocitem text="gecos:blossom" target="colours.gecos-blossom" />
+ <tocitem text="gecos:sunset" target="colours.gecos-sunset" />
+ <tocitem text="gecos:ocean" target="colours.gecos-ocean" />
<tocitem text="Hydrophobicity" target="colours.hydro" />
<tocitem text="Helix propensity" target="colours.helix" />
<tocitem text="Strand propensity" target="colours.strand" />
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Blossom Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-blossom">Blossom</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ blossom is a light color scheme with high contrast, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#8bc4b4">A</td>
+ <td bgcolor="#0893fe">C</td>
+ <td bgcolor="#5fa505">D</td>
+ <td bgcolor="#dbb501">E</td>
+</tr>
+<tr>
+ <td bgcolor="#f74fa8">F</td>
+ <td bgcolor="#00d382">G</td>
+ <td bgcolor="#ff5701">H</td>
+ <td bgcolor="#9abaf3">I</td>
+</tr>
+<tr>
+ <td bgcolor="#fea527">K</td>
+ <td bgcolor="#cda5dc">L</td>
+ <td bgcolor="#f5a1b8">M</td>
+ <td bgcolor="#b5c206">N</td>
+</tr>
+<tr>
+ <td bgcolor="#10d631">P</td>
+ <td bgcolor="#bf8527">Q</td>
+ <td bgcolor="#fc9502">R</td>
+ <td bgcolor="#7e9d59">S</td>
+</tr>
+<tr>
+ <td bgcolor="#00a29c">T</td>
+ <td bgcolor="#87c0e4">V</td>
+ <td bgcolor="#fe08fb">W</td>
+ <td bgcolor="#ff4e7a">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Flower Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-flower">Flower</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ flower is a light color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#b18a51">A</td>
+ <td bgcolor="#ff5701">C</td>
+ <td bgcolor="#01a578">D</td>
+ <td bgcolor="#2da0a1">E</td>
+</tr>
+<tr>
+ <td bgcolor="#fa559d">F</td>
+ <td bgcolor="#b1c23c">G</td>
+ <td bgcolor="#0194f9">H</td>
+ <td bgcolor="#f27663">I</td>
+</tr>
+<tr>
+ <td bgcolor="#7fc3d7">K</td>
+ <td bgcolor="#df6e75">L</td>
+ <td bgcolor="#fe9daf">M</td>
+ <td bgcolor="#0bcec6">N</td>
+</tr>
+<tr>
+ <td bgcolor="#4fa32a">P</td>
+ <td bgcolor="#7295ae">Q</td>
+ <td bgcolor="#83bff1">R</td>
+ <td bgcolor="#b4bd9b">S</td>
+</tr>
+<tr>
+ <td bgcolor="#d2b576">T</td>
+ <td bgcolor="#fd997b">V</td>
+ <td bgcolor="#ff2ded">W</td>
+ <td bgcolor="#c96ecf">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Ocean Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-ocean">Ocean</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ ocean is a blue shifted, light color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#c6ca9b">A</td>
+ <td bgcolor="#c68136">C</td>
+ <td bgcolor="#4cdfa1">D</td>
+ <td bgcolor="#60dac9">E</td>
+</tr>
+<tr>
+ <td bgcolor="#ab88ae">F</td>
+ <td bgcolor="#33a551">G</td>
+ <td bgcolor="#00cffe">H</td>
+ <td bgcolor="#f2baaa">I</td>
+</tr>
+<tr>
+ <td bgcolor="#40a090">K</td>
+ <td bgcolor="#bb8a83">L</td>
+ <td bgcolor="#a48b88">M</td>
+ <td bgcolor="#0adfc3">N</td>
+</tr>
+<tr>
+ <td bgcolor="#afd365">P</td>
+ <td bgcolor="#8bd3d1">Q</td>
+ <td bgcolor="#0ca0a8">R</td>
+ <td bgcolor="#6d9b74">S</td>
+</tr>
+<tr>
+ <td bgcolor="#8d9566">T</td>
+ <td bgcolor="#e9bea4">V</td>
+ <td bgcolor="#758aee">W</td>
+ <td bgcolor="#bac3fc">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Sunset Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-sunset">Sunset</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ sunset is a red-green color vision deficiency adapated color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#fea0fd">A</td>
+ <td bgcolor="#fc0cfe">C</td>
+ <td bgcolor="#2e7bbe">D</td>
+ <td bgcolor="#677892">E</td>
+</tr>
+<tr>
+ <td bgcolor="#ff385d">F</td>
+ <td bgcolor="#2799ff">G</td>
+ <td bgcolor="#dbc58e">H</td>
+ <td bgcolor="#fa21a1">I</td>
+</tr>
+<tr>
+ <td bgcolor="#debecc">K</td>
+ <td bgcolor="#e01e82">L</td>
+ <td bgcolor="#d13e7b">M</td>
+ <td bgcolor="#abc8f5">N</td>
+</tr>
+<tr>
+ <td bgcolor="#5766f9">P</td>
+ <td bgcolor="#8c6e81">Q</td>
+ <td bgcolor="#85746a">R</td>
+ <td bgcolor="#e7b4fd">S</td>
+</tr>
+<tr>
+ <td bgcolor="#a658b7">T</td>
+ <td bgcolor="#fe51b8">V</td>
+ <td bgcolor="#ff3701">W</td>
+ <td bgcolor="#cb5339">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
<td></td>
</tr>
<tr>
+ <td>gecos:flower</td>
+
+ <td bgcolor="#b18a51"></td>
+ <td bgcolor="#83bff1"></td>
+ <td bgcolor="#0bcec6"></td>
+ <td bgcolor="#01a578"></td>
+ <td bgcolor="#ff5701"></td>
+ <td bgcolor="#7295ae"></td>
+ <td bgcolor="#2da0a1"></td>
+ <td bgcolor="#b1c23c"></td>
+ <td bgcolor="#0194f9"></td>
+ <td bgcolor="#f27663"></td>
+ <td bgcolor="#df6e75"></td>
+ <td bgcolor="#7fc3d7"></td>
+ <td bgcolor="#fe9daf"></td>
+ <td bgcolor="#fa559d"></td>
+ <td bgcolor="#4fa32a"></td>
+ <td bgcolor="#b4bd9b"></td>
+ <td bgcolor="#d2b576"></td>
+ <td bgcolor="#ff2ded"></td>
+ <td bgcolor="#c96ecf"></td>
+ <td bgcolor="#fd997b"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:blossom</td>
+ <td bgcolor="#8bc4b4"></td>
+ <td bgcolor="#fc9502"></td>
+ <td bgcolor="#b5c206"></td>
+ <td bgcolor="#5fa505"></td>
+ <td bgcolor="#0893fe"></td>
+ <td bgcolor="#bf8527"></td>
+ <td bgcolor="#dbb501"></td>
+ <td bgcolor="#00d382"></td>
+ <td bgcolor="#ff5701"></td>
+ <td bgcolor="#9abaf3"></td>
+ <td bgcolor="#cda5dc"></td>
+ <td bgcolor="#fea527"></td>
+ <td bgcolor="#f5a1b8"></td>
+ <td bgcolor="#f74fa8"></td>
+ <td bgcolor="#10d631"></td>
+ <td bgcolor="#7e9d59"></td>
+ <td bgcolor="#00a29c"></td>
+ <td bgcolor="#fe08fb"></td>
+ <td bgcolor="#ff4e7a"></td>
+ <td bgcolor="#87c0e4"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:sunset</td>
+ <td bgcolor="#fea0fd"></td>
+ <td bgcolor="#85746a"></td>
+ <td bgcolor="#abc8f5"></td>
+ <td bgcolor="#2e7bbe"></td>
+ <td bgcolor="#fc0cfe"></td>
+ <td bgcolor="#8c6e81"></td>
+ <td bgcolor="#677892"></td>
+ <td bgcolor="#2799ff"></td>
+ <td bgcolor="#dbc58e"></td>
+ <td bgcolor="#fa21a1"></td>
+ <td bgcolor="#e01e82"></td>
+ <td bgcolor="#debecc"></td>
+ <td bgcolor="#d13e7b"></td>
+ <td bgcolor="#ff385d"></td>
+ <td bgcolor="#5766f9"></td>
+ <td bgcolor="#e7b4fd"></td>
+ <td bgcolor="#a658b7"></td>
+ <td bgcolor="#ff3701"></td>
+ <td bgcolor="#cb5339"></td>
+ <td bgcolor="#fe51b8"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:ocean</td>
+ <td bgcolor="#c6ca9b"></td>
+ <td bgcolor="#0ca0a8"></td>
+ <td bgcolor="#0adfc3"></td>
+ <td bgcolor="#4cdfa1"></td>
+ <td bgcolor="#c68136"></td>
+ <td bgcolor="#8bd3d1"></td>
+ <td bgcolor="#60dac9"></td>
+ <td bgcolor="#33a551"></td>
+ <td bgcolor="#00cffe"></td>
+ <td bgcolor="#f2baaa"></td>
+ <td bgcolor="#bb8a83"></td>
+ <td bgcolor="#40a090"></td>
+ <td bgcolor="#a48b88"></td>
+ <td bgcolor="#ab88ae"></td>
+ <td bgcolor="#afd365"></td>
+ <td bgcolor="#6d9b74"></td>
+ <td bgcolor="#8d9566"></td>
+ <td bgcolor="#758aee"></td>
+ <td bgcolor="#bac3fc"></td>
+ <td bgcolor="#e9bea4"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
<td>Hydrophobicity</td>
<td bgcolor="#ad0052"></td>
<td bgcolor="#0000ff"></td>
and the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
Defined<br>
the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
Defined<br>
git://source.jalview.org / jalview.git / commitdiff