Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
[jalview.git] / help / html / colourSchemes / index.html
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20 <head>
21 <title>Colour Schemes</title>
22 <style type="text/css">
23 <!--
24 td {
25         font-family: "Courier New", Courier, mono;
26         font-style: normal;
27         font-size: medium;
28 }
29 -->
30 </style>
31 </head>
32 <body>
33 <p><strong>Colour schemes</strong></p>
34 <p>Jalview allows the user to set a background colour for the whole
35 alignment view or for each group defined on regions within it.</p>
36 <p>To change the background colour, simply select the colour from
37 the &quot;Colour&quot; menu.</p>
38 <p>To change the colour of a group, right click on any residue
39 within a group and use the popup menu to define the group colour.</p>
40 <p>At the top of the &quot;Colour&quot; menu the tick box
41 &quot;Apply Background Colour to all groups&quot;. This is ticked by
42 default so that a chosen colour scheme will be applied to all existing
43 groups. If you wish to maintain the colour scheme for defined groups,
44 make sure you deselect this option before changing the background
45 colour.</p>
46 <p>The <strong>&quot;Colour&#8594;<a
47         href="../colourSchemes/textcolour.html">Colour Text...</a>&quot;</strong> entry
48 opens a dialog box to set a different text colour for light and dark
49 background, and the intensity threshold for transition between them.</p>
50 <p>The default colour schemes are summarised in the table below:
51 <div align="center">
52 <p>&nbsp;</p>
53 <p><strong>Protein Colour Schemes</strong></p>
54 <table border="1">
55         <tr>
56                 <td>
57                 <table border="1">
58                         <tr>
59                                 <td nowrap></td>
60                                 <td>A</td>
61                                 <td>R</td>
62                                 <td>N</td>
63                                 <td>D</td>
64                                 <td>C</td>
65                                 <td>Q</td>
66                                 <td>E</td>
67                                 <td>G</td>
68                                 <td>H</td>
69                                 <td>I</td>
70                                 <td>L</td>
71                                 <td>K</td>
72                                 <td>M</td>
73                                 <td>F</td>
74                                 <td>P</td>
75                                 <td>S</td>
76                                 <td>T</td>
77                                 <td>W</td>
78                                 <td>Y</td>
79                                 <td>V</td>
80                                 <td>B</td>
81                                 <td>X</td>
82                                 <td>Z</td>
83                         </tr>
84                         <tr>
85                                 <td height="24">Clustal</td>
86                                 <td bgcolor="#80a0f0"></td>
87                                 <td bgcolor="#f01505"></td>
88                                 <td bgcolor="#00ff00"></td>
89                                 <td bgcolor="#c048c0"></td>
90                                 <td bgcolor="#f08080"></td>
91                                 <td bgcolor="#00ff00"></td>
92                                 <td bgcolor="#c048c0"></td>
93                                 <td bgcolor="#f09048"></td>
94                                 <td bgcolor="#15a4a4"></td>
95                                 <td bgcolor="#80a0f0"></td>
96                                 <td bgcolor="#80a0f0"></td>
97                                 <td bgcolor="#f01505"></td>
98                                 <td bgcolor="#80a0f0"></td>
99                                 <td bgcolor="#80a0f0"></td>
100                                 <td bgcolor="#ffff00"></td>
101                                 <td bgcolor="#00ff00"></td>
102                                 <td bgcolor="#00ff00"></td>
103                                 <td bgcolor="#80a0f0"></td>
104                                 <td bgcolor="#15a4a4"></td>
105                                 <td bgcolor="#80a0f0"></td>
106                                 <td></td>
107                                 <td></td>
108                                 <td></td>
109                         </tr>
110                         <tr>
111                                 <td height="24">Zappo</td>
112                                 <td bgcolor="#ffafaf"></td>
113                                 <td bgcolor="#6464ff"></td>
114                                 <td bgcolor="#00ff00"></td>
115                                 <td bgcolor="#ff0000"></td>
116                                 <td bgcolor="#ffff00"></td>
117                                 <td bgcolor="#00ff00"></td>
118                                 <td bgcolor="#ff0000"></td>
119                                 <td bgcolor="#ff00ff"></td>
120                                 <td bgcolor="#6464ff"></td>
121                                 <td bgcolor="#ffafaf"></td>
122                                 <td bgcolor="#ffafaf"></td>
123                                 <td bgcolor="#6464ff"></td>
124                                 <td bgcolor="#ffafaf"></td>
125                                 <td bgcolor="#ffc800"></td>
126                                 <td bgcolor="#ff00ff"></td>
127                                 <td bgcolor="#00ff00"></td>
128                                 <td bgcolor="#00ff00"></td>
129                                 <td bgcolor="#ffc800"></td>
130                                 <td bgcolor="#ffc800"></td>
131                                 <td bgcolor="#ffafaf"></td>
132                                 <td></td>
133                                 <td></td>
134                                 <td></td>
135                         </tr>
136                         <tr>
137                                 <td>Taylor</td>
138                                 <td bgcolor="#ccff00"></td>
139                                 <td bgcolor="#0000ff"></td>
140                                 <td bgcolor="#cc00ff"></td>
141                                 <td bgcolor="#ff0000"></td>
142                                 <td bgcolor="#ffff00"></td>
143                                 <td bgcolor="#ff00cc"></td>
144                                 <td bgcolor="#ff0066"></td>
145                                 <td bgcolor="#ff9900"></td>
146                                 <td bgcolor="#0066ff"></td>
147                                 <td bgcolor="#66ff00"></td>
148                                 <td bgcolor="#33ff00"></td>
149                                 <td bgcolor="#6600ff"></td>
150                                 <td bgcolor="#00ff00"></td>
151                                 <td bgcolor="#00ff66"></td>
152                                 <td bgcolor="#ffcc00"></td>
153                                 <td bgcolor="#ff3300"></td>
154                                 <td bgcolor="#ff6600"></td>
155                                 <td bgcolor="#00ccff"></td>
156                                 <td bgcolor="#00ffcc"></td>
157                                 <td bgcolor="#99ff00"></td>
158                                 <td></td>
159                                 <td></td>
160                                 <td></td>
161                         </tr>
162                         <tr>
163                                 <td>Hydrophobicity</td>
164                                 <td bgcolor="#ad0052"></td>
165                                 <td bgcolor="#0000ff"></td>
166                                 <td bgcolor="#0c00f3"></td>
167                                 <td bgcolor="#0c00f3"></td>
168                                 <td bgcolor="#c2003d"></td>
169                                 <td bgcolor="#0c00f3"></td>
170                                 <td bgcolor="#0c00f3"></td>
171                                 <td bgcolor="#6a0095"></td>
172                                 <td bgcolor="#1500ea"></td>
173                                 <td bgcolor="#ff0000"></td>
174                                 <td bgcolor="#ea0015"></td>
175                                 <td bgcolor="#0000ff"></td>
176                                 <td bgcolor="#b0004f"></td>
177                                 <td bgcolor="#cb0034"></td>
178                                 <td bgcolor="#4600b9"></td>
179                                 <td bgcolor="#5e00a1"></td>
180                                 <td bgcolor="#61009e"></td>
181                                 <td bgcolor="#5b00a4"></td>
182                                 <td bgcolor="#4f00b0"></td>
183                                 <td bgcolor="#f60009"></td>
184                                 <td bgcolor="#0c00f3"></td>
185                                 <td bgcolor="#680097"></td>
186                                 <td bgcolor="#0c00f3"></td>
187                         </tr>
188                         <tr>
189                                 <td>Helix Propensity</td>
190                                 <td bgcolor="#e718e7"></td>
191                                 <td bgcolor="#6f906f"></td>
192                                 <td bgcolor="#1be41b"></td>
193                                 <td bgcolor="#778877"></td>
194                                 <td bgcolor="#23dc23"></td>
195                                 <td bgcolor="#926d92"></td>
196                                 <td bgcolor="#ff00ff"></td>
197                                 <td bgcolor="#00ff00"></td>
198                                 <td bgcolor="#758a75"></td>
199                                 <td bgcolor="#8a758a"></td>
200                                 <td bgcolor="#ae51ae"></td>
201                                 <td bgcolor="#a05fa0"></td>
202                                 <td bgcolor="#ef10ef"></td>
203                                 <td bgcolor="#986798"></td>
204                                 <td bgcolor="#00ff00"></td>
205                                 <td bgcolor="#36c936"></td>
206                                 <td bgcolor="#47b847"></td>
207                                 <td bgcolor="#8a758a"></td>
208                                 <td bgcolor="#21de21"></td>
209                                 <td bgcolor="#857a85"></td>
210                                 <td bgcolor="#49b649"></td>
211                                 <td bgcolor="#758a75"></td>
212                                 <td bgcolor="#c936c9"></td>
213                         </tr>
214                         <tr>
215                                 <td nowrap>Strand Propensity</td>
216                                 <td bgcolor="#5858a7"></td>
217                                 <td bgcolor="#6b6b94"></td>
218                                 <td bgcolor="#64649b"></td>
219                                 <td bgcolor="#2121de"></td>
220                                 <td bgcolor="#9d9d62"></td>
221                                 <td bgcolor="#8c8c73"></td>
222                                 <td bgcolor="#0000ff"></td>
223                                 <td bgcolor="#4949b6"></td>
224                                 <td bgcolor="#60609f"></td>
225                                 <td bgcolor="#ecec13"></td>
226                                 <td bgcolor="#b2b24d"></td>
227                                 <td bgcolor="#4747b8"></td>
228                                 <td bgcolor="#82827d"></td>
229                                 <td bgcolor="#c2c23d"></td>
230                                 <td bgcolor="#2323dc"></td>
231                                 <td bgcolor="#4949b6"></td>
232                                 <td bgcolor="#9d9d62"></td>
233                                 <td bgcolor="#c0c03f"></td>
234                                 <td bgcolor="#d3d32c"></td>
235                                 <td bgcolor="#ffff00"></td>
236                                 <td bgcolor="#4343bc"></td>
237                                 <td bgcolor="#797986"></td>
238                                 <td bgcolor="#4747b8"></td>
239                         </tr>
240                         <tr>
241                                 <td>Turn Propensity</td>
242                                 <td bgcolor="#2cd3d3"></td>
243                                 <td bgcolor="#708f8f"></td>
244                                 <td bgcolor="#ff0000"></td>
245                                 <td bgcolor="#e81717"></td>
246                                 <td bgcolor="#a85757"></td>
247                                 <td bgcolor="#3fc0c0"></td>
248                                 <td bgcolor="#778888"></td>
249                                 <td bgcolor="#ff0000"></td>
250                                 <td bgcolor="#708f8f"></td>
251                                 <td bgcolor="#00ffff"></td>
252                                 <td bgcolor="#1ce3e3"></td>
253                                 <td bgcolor="#7e8181"></td>
254                                 <td bgcolor="#1ee1e1"></td>
255                                 <td bgcolor="#1ee1e1"></td>
256                                 <td bgcolor="#f60909"></td>
257                                 <td bgcolor="#e11e1e"></td>
258                                 <td bgcolor="#738c8c"></td>
259                                 <td bgcolor="#738c8c"></td>
260                                 <td bgcolor="#9d6262"></td>
261                                 <td bgcolor="#07f8f8"></td>
262                                 <td bgcolor="#f30c0c"></td>
263                                 <td bgcolor="#7c8383"></td>
264                                 <td bgcolor="#5ba4a4"></td>
265                         </tr>
266                         <tr>
267                                 <td>Buried Index</td>
268                                 <td bgcolor="#00a35c"></td>
269                                 <td bgcolor="#00fc03"></td>
270                                 <td bgcolor="#00eb14"></td>
271                                 <td bgcolor="#00eb14"></td>
272                                 <td bgcolor="#0000ff"></td>
273                                 <td bgcolor="#00f10e"></td>
274                                 <td bgcolor="#00f10e"></td>
275                                 <td bgcolor="#009d62"></td>
276                                 <td bgcolor="#00d52a"></td>
277                                 <td bgcolor="#0054ab"></td>
278                                 <td bgcolor="#007b84"></td>
279                                 <td bgcolor="#00ff00"></td>
280                                 <td bgcolor="#009768"></td>
281                                 <td bgcolor="#008778"></td>
282                                 <td bgcolor="#00e01f"></td>
283                                 <td bgcolor="#00d52a"></td>
284                                 <td bgcolor="#00db24"></td>
285                                 <td bgcolor="#00a857"></td>
286                                 <td bgcolor="#00e619"></td>
287                                 <td bgcolor="#005fa0"></td>
288                                 <td bgcolor="#00eb14"></td>
289                                 <td bgcolor="#00b649"></td>
290                                 <td bgcolor="#00f10e"></td>
291                         </tr>
292                 </table>
293                 </td>
294         </tr>
295 </table>
296 <p>&nbsp;</p>
297 <p><strong>Nucleotide Colour Schemes</strong></p>
298 <table border="1">
299         <tr>
300                 <td>
301                 <table border="1">
302                         <tr>
303                                 <td nowrap></td>
304                                 <td>A</td> <!--Adenine-->
305                             <td>C</td> <!--Cytosine-->
306                         <td>G</td> <!--Guanine-->
307                         <td>T</td> <!--Thymine-->
308                         <td>U</td> <!--Uracil-->
309                         <td>I</td> <!--Inosine-->
310                         <td>X</td> <!--Xanthine-->
311                         <td>R</td> <!--Unknown Purine-->
312                         <td>Y</td> <!--Unknown Pyrimidine-->
313                         <td>N</td> <!--Unknown-->
314                         <td>W</td> <!--Weak nucleotide (A or T)-->
315                         <td>S</td> <!--Strong nucleotide (G or C)-->
316                         <td>M</td> <!--Amino (A or C)-->
317                         <td>K</td> <!--Keto (G or T)-->
318                         <td>B</td> <!--Not A (G or C or T)-->
319                         <td>H</td> <!--Not G (A or C or T)-->
320                         <td>D</td> <!--Not C (A or G or T)-->
321                         <td>V</td> <!--Not T (A or G or C-->
322                         </tr>
323                         <tr>
324                                 <td height="24">Nucleotide</td>
325                                 <td bgcolor="#64F73F"></td>
326                                 <td bgcolor="#FFB340"></td>
327                         <td bgcolor="#EB413C"></td>
328                         <td bgcolor="#3C88EE"></td>
329                         <td bgcolor="#3C88EE"></td>
330                         <td></td>
331                         <td></td>
332                         <td></td>
333                         <td></td>
334                         <td></td>
335                         <td></td>
336                         <td></td>
337                         <td></td>
338                         <td></td>
339                         <td></td>
340                         <td></td>
341                         <td></td>
342                         <td></td>
343                         </tr>
344                         <tr>
345                                 <td height="24">Purine/Pyrimidine</td>
346                                 <td bgcolor="#FF83FA"></td>
347                                 <td bgcolor="#40E0D0"></td>
348                         <td bgcolor="#FF83FA"></td>
349                         <td bgcolor="#40E0D0"></td>
350                         <td bgcolor="#40E0D0"></td>
351                         <td></td>
352                         <td></td>
353                         <td bgcolor="#FF83FA"></td>
354                         <td bgcolor="#40E0D0"></td>
355                         <td></td>
356                         <td></td>
357                         <td></td>
358                         <td></td>
359                         <td></td>
360                         <td></td>
361                         <td></td>
362                         <td></td>
363                         <td></td>
364                         </tr>
365                 </table>
366                 </td>
367         </tr>
368 </table>
369
370
371 </div>
372 <p align="center">&nbsp;</p>
373 </body>
374 </html>