Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_de...
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22 <head>
23 <title>Colour Schemes</title>
24 <style type="text/css">
25 <!--
26 td {
27         font-family: "Courier New", Courier, mono;
28         font-style: normal;
29         font-size: medium;
30 }
31 -->
32 </style>
33 </head>
34 <body>
35   <p>
36     <strong>Colour schemes</strong>
37   </p>
38   <p>Jalview allows the user to set a colour scheme for the
39     whole alignment view or for each group defined on regions within it.</p>
40   <p>To change the colour for a view, simply select a new colour scheme from
41     the &quot;Colour&quot; menu.</p>
42   <p>To change the colour of a group, right click on any residue
43     within a group and use the popup menu to define the group colour.</p>
44   <p>At the top of the &quot;Colour&quot; menu you'll see a tick box
45     &quot;Apply Colour to all groups&quot;. This is ticked by
46     default so that a chosen colour scheme will be applied to all
47     existing groups. If you wish to maintain the colour scheme for
48     defined groups, make sure you deselect this option before selecting
49     a new scheme in the Colour menu.</p>
50   <p>
51     The <strong>&quot;Colour&#8594;<a
52       href="textcolour.html">Colour Text...</a>&quot;
53     </strong> entry opens a dialog box to set a different text colour for light
54     and dark background, and the intensity threshold for transition
55     between them.
56   </p>
57         <p>
58                 <strong>Dynamic colour schemes</strong>
59         </p>
60         <p>
61                 Alignments and groups may be coloured according to <a
62                         href="annotationColouring.html">associated sequence and alignment
63                         annotation</a>. Any applied colour schemes (such as those shown in the
64                 table below) can also be <a href="conservation.html">shaded by
65                         amino acid physico-chemical property conservation</a> to reveal patterns
66                 of variation, or applied selectively to <a href="abovePID.html">Above
67                         Identity Threshold</a>.
68         </p>
69         <p>
70                 Alignments and groups can also be shaded according to percentage
71                 abundance of aligned residues (using <a href="pid.html">Percentage
72                         Identity</a>), and for protein alignments, the <a href="blosum.html">BLOSUM
73                         62 Score</a> and <a href="clustal.html">ClustalX</a> shading schemes
74                 highlight amino acid conservation.
75         </p>
76         <p>
77                 The <strong>Sequence ID</strong> colour scheme shades sequences with
78                 the same colour assigned to their Sequence ID. Colours are assigned
79                 when groups are created by <a href="../calculations/treeviewer.html">partitioning
80                         a tree</a> or subdividing the alignment by sequence with <strong>Select&#8594;Make
81                         Groups For Selection</strong>.
82         </p>
83         <p>
84                 <strong>Amino acid and Nucleotide based colour schemes</strong>
85         <p>The built-in colour schemes based on amino acid and nucleotide symbols are
86                 summarised in the table below:
87         
88         <div align="center"><p>&nbsp;</p>
89                 <p>
90                         <strong>Protein Colour Schemes</strong>
91                 </p>
92                 <table border="1">
93                         <tr>
94                                 <td>
95                                         <table border="1">
96                                                 <tr>
97                                                         <td nowrap></td>
98                                                         <td>A</td>
99                                                         <td>R</td>
100                                                         <td>N</td>
101                                                         <td>D</td>
102                                                         <td>C</td>
103                                                         <td>Q</td>
104                                                         <td>E</td>
105                                                         <td>G</td>
106                                                         <td>H</td>
107                                                         <td>I</td>
108                                                         <td>L</td>
109                                                         <td>K</td>
110                                                         <td>M</td>
111                                                         <td>F</td>
112                                                         <td>P</td>
113                                                         <td>S</td>
114                                                         <td>T</td>
115                                                         <td>W</td>
116                                                         <td>Y</td>
117                                                         <td>V</td>
118                                                         <td>B</td>
119                                                         <td>X</td>
120                                                         <td>Z</td>
121                                                 </tr>
122                                                 <tr>
123                                                         <td height="24">Clustal</td>
124                                                         <td bgcolor="#80a0f0"></td>
125                                                         <td bgcolor="#f01505"></td>
126                                                         <td bgcolor="#00ff00"></td>
127                                                         <td bgcolor="#c048c0"></td>
128                                                         <td bgcolor="#f08080"></td>
129                                                         <td bgcolor="#00ff00"></td>
130                                                         <td bgcolor="#c048c0"></td>
131                                                         <td bgcolor="#f09048"></td>
132                                                         <td bgcolor="#15a4a4"></td>
133                                                         <td bgcolor="#80a0f0"></td>
134                                                         <td bgcolor="#80a0f0"></td>
135                                                         <td bgcolor="#f01505"></td>
136                                                         <td bgcolor="#80a0f0"></td>
137                                                         <td bgcolor="#80a0f0"></td>
138                                                         <td bgcolor="#ffff00"></td>
139                                                         <td bgcolor="#00ff00"></td>
140                                                         <td bgcolor="#00ff00"></td>
141                                                         <td bgcolor="#80a0f0"></td>
142                                                         <td bgcolor="#15a4a4"></td>
143                                                         <td bgcolor="#80a0f0"></td>
144                                                         <td></td>
145                                                         <td></td>
146                                                         <td></td>
147                                                 </tr>
148                                                 <tr>
149                                                         <td height="24">Zappo</td>
150                                                         <td bgcolor="#ffafaf"></td>
151                                                         <td bgcolor="#6464ff"></td>
152                                                         <td bgcolor="#00ff00"></td>
153                                                         <td bgcolor="#ff0000"></td>
154                                                         <td bgcolor="#ffff00"></td>
155                                                         <td bgcolor="#00ff00"></td>
156                                                         <td bgcolor="#ff0000"></td>
157                                                         <td bgcolor="#ff00ff"></td>
158                                                         <td bgcolor="#6464ff"></td>
159                                                         <td bgcolor="#ffafaf"></td>
160                                                         <td bgcolor="#ffafaf"></td>
161                                                         <td bgcolor="#6464ff"></td>
162                                                         <td bgcolor="#ffafaf"></td>
163                                                         <td bgcolor="#ffc800"></td>
164                                                         <td bgcolor="#ff00ff"></td>
165                                                         <td bgcolor="#00ff00"></td>
166                                                         <td bgcolor="#00ff00"></td>
167                                                         <td bgcolor="#ffc800"></td>
168                                                         <td bgcolor="#ffc800"></td>
169                                                         <td bgcolor="#ffafaf"></td>
170                                                         <td></td>
171                                                         <td></td>
172                                                         <td></td>
173                                                 </tr>
174                                                 <tr>
175                                                         <td>Taylor</td>
176                                                         <td bgcolor="#ccff00"></td>
177                                                         <td bgcolor="#0000ff"></td>
178                                                         <td bgcolor="#cc00ff"></td>
179                                                         <td bgcolor="#ff0000"></td>
180                                                         <td bgcolor="#ffff00"></td>
181                                                         <td bgcolor="#ff00cc"></td>
182                                                         <td bgcolor="#ff0066"></td>
183                                                         <td bgcolor="#ff9900"></td>
184                                                         <td bgcolor="#0066ff"></td>
185                                                         <td bgcolor="#66ff00"></td>
186                                                         <td bgcolor="#33ff00"></td>
187                                                         <td bgcolor="#6600ff"></td>
188                                                         <td bgcolor="#00ff00"></td>
189                                                         <td bgcolor="#00ff66"></td>
190                                                         <td bgcolor="#ffcc00"></td>
191                                                         <td bgcolor="#ff3300"></td>
192                                                         <td bgcolor="#ff6600"></td>
193                                                         <td bgcolor="#00ccff"></td>
194                                                         <td bgcolor="#00ffcc"></td>
195                                                         <td bgcolor="#99ff00"></td>
196                                                         <td></td>
197                                                         <td></td>
198                                                         <td></td>
199                                                 </tr>
200                                                 <tr>
201                                                         <td>Hydrophobicity</td>
202                                                         <td bgcolor="#ad0052"></td>
203                                                         <td bgcolor="#0000ff"></td>
204                                                         <td bgcolor="#0c00f3"></td>
205                                                         <td bgcolor="#0c00f3"></td>
206                                                         <td bgcolor="#c2003d"></td>
207                                                         <td bgcolor="#0c00f3"></td>
208                                                         <td bgcolor="#0c00f3"></td>
209                                                         <td bgcolor="#6a0095"></td>
210                                                         <td bgcolor="#1500ea"></td>
211                                                         <td bgcolor="#ff0000"></td>
212                                                         <td bgcolor="#ea0015"></td>
213                                                         <td bgcolor="#0000ff"></td>
214                                                         <td bgcolor="#b0004f"></td>
215                                                         <td bgcolor="#cb0034"></td>
216                                                         <td bgcolor="#4600b9"></td>
217                                                         <td bgcolor="#5e00a1"></td>
218                                                         <td bgcolor="#61009e"></td>
219                                                         <td bgcolor="#5b00a4"></td>
220                                                         <td bgcolor="#4f00b0"></td>
221                                                         <td bgcolor="#f60009"></td>
222                                                         <td bgcolor="#0c00f3"></td>
223                                                         <td bgcolor="#680097"></td>
224                                                         <td bgcolor="#0c00f3"></td>
225                                                 </tr>
226                                                 <tr>
227                                                         <td>Helix Propensity</td>
228                                                         <td bgcolor="#e718e7"></td>
229                                                         <td bgcolor="#6f906f"></td>
230                                                         <td bgcolor="#1be41b"></td>
231                                                         <td bgcolor="#778877"></td>
232                                                         <td bgcolor="#23dc23"></td>
233                                                         <td bgcolor="#926d92"></td>
234                                                         <td bgcolor="#ff00ff"></td>
235                                                         <td bgcolor="#00ff00"></td>
236                                                         <td bgcolor="#758a75"></td>
237                                                         <td bgcolor="#8a758a"></td>
238                                                         <td bgcolor="#ae51ae"></td>
239                                                         <td bgcolor="#a05fa0"></td>
240                                                         <td bgcolor="#ef10ef"></td>
241                                                         <td bgcolor="#986798"></td>
242                                                         <td bgcolor="#00ff00"></td>
243                                                         <td bgcolor="#36c936"></td>
244                                                         <td bgcolor="#47b847"></td>
245                                                         <td bgcolor="#8a758a"></td>
246                                                         <td bgcolor="#21de21"></td>
247                                                         <td bgcolor="#857a85"></td>
248                                                         <td bgcolor="#49b649"></td>
249                                                         <td bgcolor="#758a75"></td>
250                                                         <td bgcolor="#c936c9"></td>
251                                                 </tr>
252                                                 <tr>
253                                                         <td nowrap>Strand Propensity</td>
254                                                         <td bgcolor="#5858a7"></td>
255                                                         <td bgcolor="#6b6b94"></td>
256                                                         <td bgcolor="#64649b"></td>
257                                                         <td bgcolor="#2121de"></td>
258                                                         <td bgcolor="#9d9d62"></td>
259                                                         <td bgcolor="#8c8c73"></td>
260                                                         <td bgcolor="#0000ff"></td>
261                                                         <td bgcolor="#4949b6"></td>
262                                                         <td bgcolor="#60609f"></td>
263                                                         <td bgcolor="#ecec13"></td>
264                                                         <td bgcolor="#b2b24d"></td>
265                                                         <td bgcolor="#4747b8"></td>
266                                                         <td bgcolor="#82827d"></td>
267                                                         <td bgcolor="#c2c23d"></td>
268                                                         <td bgcolor="#2323dc"></td>
269                                                         <td bgcolor="#4949b6"></td>
270                                                         <td bgcolor="#9d9d62"></td>
271                                                         <td bgcolor="#c0c03f"></td>
272                                                         <td bgcolor="#d3d32c"></td>
273                                                         <td bgcolor="#ffff00"></td>
274                                                         <td bgcolor="#4343bc"></td>
275                                                         <td bgcolor="#797986"></td>
276                                                         <td bgcolor="#4747b8"></td>
277                                                 </tr>
278                                                 <tr>
279                                                         <td>Turn Propensity</td>
280                                                         <td bgcolor="#2cd3d3"></td>
281                                                         <td bgcolor="#708f8f"></td>
282                                                         <td bgcolor="#ff0000"></td>
283                                                         <td bgcolor="#e81717"></td>
284                                                         <td bgcolor="#a85757"></td>
285                                                         <td bgcolor="#3fc0c0"></td>
286                                                         <td bgcolor="#778888"></td>
287                                                         <td bgcolor="#ff0000"></td>
288                                                         <td bgcolor="#708f8f"></td>
289                                                         <td bgcolor="#00ffff"></td>
290                                                         <td bgcolor="#1ce3e3"></td>
291                                                         <td bgcolor="#7e8181"></td>
292                                                         <td bgcolor="#1ee1e1"></td>
293                                                         <td bgcolor="#1ee1e1"></td>
294                                                         <td bgcolor="#f60909"></td>
295                                                         <td bgcolor="#e11e1e"></td>
296                                                         <td bgcolor="#738c8c"></td>
297                                                         <td bgcolor="#738c8c"></td>
298                                                         <td bgcolor="#9d6262"></td>
299                                                         <td bgcolor="#07f8f8"></td>
300                                                         <td bgcolor="#f30c0c"></td>
301                                                         <td bgcolor="#7c8383"></td>
302                                                         <td bgcolor="#5ba4a4"></td>
303                                                 </tr>
304                                                 <tr>
305                                                         <td>Buried Index</td>
306                                                         <td bgcolor="#00a35c"></td>
307                                                         <td bgcolor="#00fc03"></td>
308                                                         <td bgcolor="#00eb14"></td>
309                                                         <td bgcolor="#00eb14"></td>
310                                                         <td bgcolor="#0000ff"></td>
311                                                         <td bgcolor="#00f10e"></td>
312                                                         <td bgcolor="#00f10e"></td>
313                                                         <td bgcolor="#009d62"></td>
314                                                         <td bgcolor="#00d52a"></td>
315                                                         <td bgcolor="#0054ab"></td>
316                                                         <td bgcolor="#007b84"></td>
317                                                         <td bgcolor="#00ff00"></td>
318                                                         <td bgcolor="#009768"></td>
319                                                         <td bgcolor="#008778"></td>
320                                                         <td bgcolor="#00e01f"></td>
321                                                         <td bgcolor="#00d52a"></td>
322                                                         <td bgcolor="#00db24"></td>
323                                                         <td bgcolor="#00a857"></td>
324                                                         <td bgcolor="#00e619"></td>
325                                                         <td bgcolor="#005fa0"></td>
326                                                         <td bgcolor="#00eb14"></td>
327                                                         <td bgcolor="#00b649"></td>
328                                                         <td bgcolor="#00f10e"></td>
329                                                 </tr>
330                                         </table>
331                                 </td>
332                         </tr>
333                 </table>
334                 <p>&nbsp;</p>
335                 <p>
336                         <strong>Nucleotide Colour Schemes</strong>
337                 </p>
338                 <table border="1">
339                         <tr>
340                                 <td>
341                                         <table border="1">
342                                                 <tr>
343                                                         <td nowrap></td>
344                                                         <td>A</td>
345                                                         <!--Adenine-->
346                                                         <td>C</td>
347                                                         <!--Cytosine-->
348                                                         <td>G</td>
349                                                         <!--Guanine-->
350                                                         <td>T</td>
351                                                         <!--Thymine-->
352                                                         <td>U</td>
353                                                         <!--Uracil-->
354                                                         <td>I</td>
355                                                         <!--Inosine-->
356                                                         <td>X</td>
357                                                         <!--Xanthine-->
358                                                         <td>R</td>
359                                                         <!--Unknown Purine-->
360                                                         <td>Y</td>
361                                                         <!--Unknown Pyrimidine-->
362                                                         <td>N</td>
363                                                         <!--Unknown-->
364                                                         <td>W</td>
365                                                         <!--Weak nucleotide (A or T)-->
366                                                         <td>S</td>
367                                                         <!--Strong nucleotide (G or C)-->
368                                                         <td>M</td>
369                                                         <!--Amino (A or C)-->
370                                                         <td>K</td>
371                                                         <!--Keto (G or T)-->
372                                                         <td>B</td>
373                                                         <!--Not A (G or C or T)-->
374                                                         <td>H</td>
375                                                         <!--Not G (A or C or T)-->
376                                                         <td>D</td>
377                                                         <!--Not C (A or G or T)-->
378                                                         <td>V</td>
379                                                         <!--Not T (A or G or C-->
380                                                 </tr>
381                                                 <tr>
382                                                         <td height="24">Nucleotide</td>
383                                                         <td bgcolor="#64F73F"></td>
384                                                         <td bgcolor="#FFB340"></td>
385                                                         <td bgcolor="#EB413C"></td>
386                                                         <td bgcolor="#3C88EE"></td>
387                                                         <td bgcolor="#3C88EE"></td>
388                                                         <td></td>
389                                                         <td></td>
390                                                         <td></td>
391                                                         <td></td>
392                                                         <td></td>
393                                                         <td></td>
394                                                         <td></td>
395                                                         <td></td>
396                                                         <td></td>
397                                                         <td></td>
398                                                         <td></td>
399                                                         <td></td>
400                                                         <td></td>
401                                                 </tr>
402                                                 <tr>
403                                                         <td height="24">Purine/Pyrimidine</td>
404                                                         <td bgcolor="#FF83FA"></td>
405                                                         <td bgcolor="#40E0D0"></td>
406                                                         <td bgcolor="#FF83FA"></td>
407                                                         <td bgcolor="#40E0D0"></td>
408                                                         <td bgcolor="#40E0D0"></td>
409                                                         <td></td>
410                                                         <td></td>
411                                                         <td bgcolor="#FF83FA"></td>
412                                                         <td bgcolor="#40E0D0"></td>
413                                                         <td></td>
414                                                         <td></td>
415                                                         <td></td>
416                                                         <td></td>
417                                                         <td></td>
418                                                         <td></td>
419                                                         <td></td>
420                                                         <td></td>
421                                                         <td></td>
422                                                 </tr>
423                                         </table>
424                                 </td>
425                         </tr>
426                 </table>
427
428
429         </div>
430         <p align="center">&nbsp;</p>
431 </body>
432 </html>