help/help/html/colourSchemes/index.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  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>