help/html/menus/alignmentMenu.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>Alignment Window Menus</title>
  24 </head>
  25
  26 <body>
  27         <p>
  28                 <strong>Alignment Window Menus</strong>
  29         </p>
  30         <ul>
  31                 <li><strong>File</strong>
  32                         <ul>
  33                                 <li><strong>Fetch Sequence</strong><br> <em>Shows a
  34                                                 dialog window in which you can retrieve known ids from Uniprot,
  35                                                 EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
  36                                                 European Bioinformatics Institute. See <a
  37                                                 href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
  38                                 <li><strong>Add Sequences</strong><em><br> Add
  39                                                 sequences to the visible alignment from file, URL, or cut &amp;
  40                                                 paste window </em>
  41                                 </li>
  42                                 <li><strong>Reload</strong><em><br> Reloads the
  43                                                 alignment from the original file, if available.<br> <strong>Warning:
  44                                                         This will delete any edits, analyses and colourings applied since
  45                                                         the alignment was last saved, and cannot be undone.</strong> </em>
  46                                 </li>
  47                                 <li><strong>Save (Control S)</strong><em><br> Saves
  48                                                 the alignment to the file it was loaded from (if available), in
  49                                                 the same format, updating the original in place. </em>
  50                                 </li>
  51                                 <li><strong>Save As (Control Shift S)<br> </strong><em>Save
  52                                                 the alignment to local file. A file selection window will open,
  53                                                 use the &quot;Files of type:&quot; selection box to determine
  54                                                 which <a href="../io/index.html">alignment format</a> to save as.</em>
  55                                 </li>
  56                                 <li><strong>Output to Textbox<br> </strong><em>The
  57                                                 alignment will be displayed in plain text in a new window, which
  58                                                 you can &quot;Copy and Paste&quot; using the pull down menu, or
  59                                                 your standard operating system copy and paste keys. The output
  60                                                 window also has a <strong>&quot;New Window&quot;</strong> button
  61                                                 to import the (possibly edited) text as a new alignment.<br>
  62                                                 Select the format of the text by selecting one of the following
  63                                                 menu items.</em>
  64                                         <ul>
  65                                                 <li><strong>FASTA</strong> </li>
  66                                                 <li><strong>MSF</strong></li>
  67                                                 <li><strong>CLUSTAL</strong></li>
  68                                                 <li><strong>BLC</strong></li>
  69                                                 <li><strong>PIR</strong></li>
  70                                                 <li><strong>PFAM</strong></li>
  71                                                 <li><strong>PileUp</strong></li>
  72                                                 <li><strong>AMSA</strong></li>
  73                                                 <li><strong>STH</strong></li>
  74                                                 <li><strong>Phylip</strong></li>
  75                                                 <li><strong>JSON</strong></li>
  76                                         </ul></li>
  77                                 <li><strong>Print (Control P)<br> </strong><em>Jalview
  78                                                 will print the alignment using the current fonts and colours of
  79                                                 your alignment. If the alignment has annotations visible, these
  80                                                 will be printed below the alignment. If the alignment is wrapped
  81                                                 the number of residues per line of your alignment will depend on
  82                                                 the paper width or your alignment window width, whichever is the
  83                                                 smaller. </em>
  84                                 </li>
  85                                 <li><strong>Export Image</strong> <em><br> Creates an
  86                                                 alignment graphic with the current view's annotation, alignment
  87                                                 background colours and group colours. If the alignment is <a
  88                                                 href="../features/wrap.html">wrapped</a>, the output will also be
  89                                                 wrapped and will have the same visible residue width as the open
  90                                                 alignment. </em>
  91                                         <ul>
  92                                                 <li><strong>HTML<br> </strong><em>Create a <a
  93                                                                 href="../io/export.html">web page</a> from your alignment.</em>
  94                                                 </li>
  95                                                 <li><strong>EPS<br> </strong><em>Create an <a
  96                                                                 href="../io/export.html">Encapsulated Postscript</a> file from
  97                                                                 your alignment.</em>
  98                                                 </li>
  99                                                 <li><strong>PNG<br> </strong><em>Create a <a
 100                                                                 href="../io/export.html">Portable Network Graphics</a> file from
 101                                                                 your alignment.</em>
 102                                                 </li>
 103                                         </ul></li>
 104                                 <li><strong>Export Features</strong><em><br> All
 105                                                 features visible on the alignment can be saved to file or
 106                                                 displayed in a textbox in either Jalview or GFF format</em>
 107                                 </li>
 108                                 <li><strong>Export Annotations</strong><em><br> All
 109                                                 annotations visible on the alignment can be saved to file or
 110                                                 displayed in a textbox in Jalview annotations format. </em>
 111                                 </li>
 112                                 <li><strong>Load Associated Tree<br> </strong><em>Jalview
 113                                                 can <a href="../calculations/treeviewer.html">view trees</a>
 114                                                  stored in the Newick file format, and associate them with the
 115                                                 alignment. Note: the ids of the tree file and your alignment MUST
 116                                                 be the same.</em></li>
 117                                 <li><strong>Load Features / Annotations<br> </strong><em>Load
 118                                                 files describing precalculated <a
 119                                                 href="../features/featuresFormat.html">sequence features</a> or <a
 120                                                 href="../features/annotationsFormat.html">alignment
 121                                                         annotations</a>.</em></li>
 122                                 <li><strong>Close (Control W)</strong><br> <em>Close
 123                                                 the alignment window. Make sure you have saved your alignment
 124                                                 before you close - either as a Jalview project or by using the <strong>Save
 125                                                         As</strong> menu.</em>
 126                                 </li>
 127                         </ul></li>
 128                 <li><strong>Edit</strong>
 129                         <ul>
 130                                 <li><strong>Undo (Control Z)</strong><em><br> This
 131                                                 will undo any edits you make to the alignment. This applies to
 132                                                 insertion or deletion of gaps, cutting residues or sequences from
 133                                                 the alignment or pasting sequences to the current alignment or
 134                                                 sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
 135                                                 colour changes, adjustments to group sizes, or changes to the
 136                                                 annotation panel. </em>
 137                                 </li>
 138                                 <li><strong>Redo (Control Y)<br> </strong><em>Any
 139                                                 actions which you undo can be redone using redo. </em>
 140                                 </li>
 141                                 <li><strong>Cut (Control X)<br> </strong><em>This
 142                                                 will make a copy of the currently selected residues before
 143                                                 removing them from your alignment. Click on a sequence name if you
 144                                                 wish to select a whole sequence. <br> Use &lt;CTRL&gt; and X
 145                                                 (&lt;APPLE&gt; and X on MacOSX) to cut.</em>
 146                                 </li>
 147                                 <li><strong>Copy (Control C)</strong><br> <em>Copies
 148                                                 the currently selected residues to the system clipboard - you can
 149                                                 also do this by pressing &lt;CTRL&gt; and C (&lt;APPLE&gt; and C
 150                                                 on MacOSX). <br> If you try to paste the clipboard contents
 151                                                 to a text editor, you will see the format of the copied residues
 152                                                 FASTA.</em></li>
 153                                 <li><strong>Paste </strong>
 154                                         <ul>
 155                                                 <li><strong>To New Alignment (Control Shift V)<br>
 156                                                 </strong><em>A new alignment window will be created from sequences
 157                                                                 previously copied or cut to the system clipboard. <br> Use
 158                                                                 &lt;CTRL&gt; and &lt;SHIFT&gt; and V(&lt;APPLE&gt; and
 159                                                                 &lt;SHIFT;&gt; and and V on MacOSX) to paste.</em>
 160                                                 </li>
 161                                                 <li><strong>Add To This Alignment (Control V)<br>
 162                                                 </strong><em>Copied sequences from another alignment window can be
 163                                                                 added to the current Jalview alignment. </em>
 164                                                 </li>
 165                                         </ul></li>
 166                                 <li><strong>Delete (Backspace)<br> </strong><em>This
 167                                                 will delete the currently selected residues without copying them
 168                                                 to the clipboard. Like the other edit operations, this can be
 169                                                 undone with <strong>Undo</strong>.</em>
 170                                 </li>
 171                                 <li><strong>Remove Left (Control L)<br> </strong><em>If
 172                                                 the alignment has marked columns, the alignment will be trimmed to
 173                                                 the left of the leftmost marked column. To mark a column, mouse
 174                                                 click the scale bar above the alignment. Click again to unmark a
 175                                                 column, or select &quot;Deselect All&quot; to deselect all
 176                                                 columns.</em></li>
 177                                 <li><strong>Remove Right (Control R)<br> </strong><em>If
 178                                                 the alignment has marked columns, the alignment will be trimmed to
 179                                                 the left of the leftmost marked column. To mark a column, mouse
 180                                                 click the scale bar above the alignment. Click again to unmark a
 181                                                 column, or select &quot;Deselect All&quot; to deselect all
 182                                                 columns.</em></li>
 183                                 <li><strong>Remove Empty Columns (Control E)<br>
 184                                 </strong><em>All columns which only contain gap characters
 185                                                 (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You may
 186                                                 set the default gap character in <a
 187                                                 href="../features/preferences.html">preferences</a>. </em>
 188                                 </li>
 189                                 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
 190                                         <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
 191                                                 deleted from the selected area of the alignment. If no selection
 192                                                 is made, ALL the gaps in the alignment will be removed.<br>
 193                                                 You may set the default gap character in <a
 194                                                 href="../features/preferences.html">preferences</a>. </em>
 195                                 </li>
 196                                 <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
 197                                                 this option brings up a window asking you to select a threshold.
 198                                                 If the percentage identity between any two sequences (under the
 199                                                 current alignment) exceeds this value then one of the sequences
 200                                                 (the shorter) is discarded. Press the &quot;Apply&quot; button to
 201                                                 remove redundant sequences. The &quot;Undo&quot; button will undo
 202                                                 the last redundancy deletion.</em>
 203                                 </li>
 204                                 <li><strong>Pad Gaps<br> </strong><em>When selected,
 205                                                 the alignment will be kept at minimal width (so there are no empty
 206                                                 columns before or after the first or last aligned residue) and all
 207                                                 sequences will be padded with gap characters before and
 208                                                 after their terminating residues.<br> This switch is useful
 209                                                 when making a tree using unaligned sequences and when working with
 210                                                 alignment analysis programs which require 'properly aligned
 211                                                 sequences' to be all the same length.<br> You may set the
 212                                                 default for <strong>Pad Gaps</strong> in the <a
 213                                                 href="../features/preferences.html">preferences</a>. </em>
 214                                 </li>
 215                         </ul></li>
 216                 <li><strong>Select</strong>
 217                         <ul>
 218                                 <li><strong><a href="../features/search.html">Find...
 219                                                         (Control F)</a> </strong><em><br> Opens the Find dialog box to
 220                                                 search for residues, sequence name or residue position within the
 221                                                 alignment and create new sequence features from the queries. </em>
 222                                 </li>
 223                                 <li><strong>Select All (Control A)<br> </strong><em>Selects
 224                                                 all the sequences and residues in the alignment. <br> Use
 225                                                 &lt;CTRL&gt; and A (&lt;APPLE&gt; and A on a MacOSX) to select
 226                                                 all.</em></li>
 227                                 <li><strong>Deselect All (Escape)<br> </strong><em>Removes
 228                                                 the current selection box (red dashed box) from the alignment
 229                                                 window. All selected sequences, residues and marked columns will
 230                                                 be deselected. </em><em> <br> Use &lt;ESCAPE&gt; to deselect
 231                                                 all.</em></li>
 232                                 <li><strong>Invert Sequence Selection (Control I)<br>
 233                                 </strong><em>Any sequence ids currently not selected will replace the
 234                                                 current selection. </em>
 235                                 </li>
 236                                 <li><strong>Invert Column Selection (Control Alt I)<br>
 237                                 </strong><em>Any columns currently not selected will replace the current
 238                                                 column selection. </em>
 239                                 </li>
 240                                   <li><strong>Create Group (Control G)<br></strong>
 241   <em>Create a group containing the currently selected sequences.</em></li>
 242   <li><strong>Remove Group (Shift Control G)<br></strong>
 243   <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
 244                         <li><strong>Make Groups for selection<br /> </strong> <em>The currently
 245                                                 selected groups of the alignment will be subdivided according to
 246                                                 the contents of the currently selected region. <br />Use this to
 247                                                 subdivide an alignment based on the different combinations of
 248                                                 residues observed at specific positions. (new in jalview 2.5)</em>
 249                                 </li>
 250         <li><strong>Undefine Groups (Control U)<br> </strong><em>The
 251             alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
 252             This cannot be undone.</em>
 253         </li>
 254                 </ul></li>
 255                 <li><strong>View</strong>
 256                         <ul>
 257                                 <li><strong>New View (Control T)</strong><em><br>
 258                                                 Creates a new view from the current alignment view. </em>
 259                                 </li>
 260                                 <li><strong>Expand Views (X)</strong><em><br> Display
 261                                                 each view associated with the alignment in its own alignment
 262                                                 window, allowing several views to be displayed simultaneously. </em>
 263                                 </li>
 264                                 <li><strong>Gather Views (G)</strong><em><br> Each
 265                                                 view associated with the alignment will be displayed within its
 266                                                 own tab on the current alignment window. </em>
 267                                 </li>
 268                                 <li><strong>Show&#8594;(all Columns / Sequences /
 269                                                 Sequences and Columns)</strong><em><br> All hidden Columns /
 270                                                 Sequences / Sequences and Columns will be revealed. </em>
 271                                 </li>
 272                                 <li><strong>Hide&#8594;(all Columns / Sequences /
 273                                                 Selected Region / All but Selected Region )</strong><em><br>
 274                                                 Hides the all the currently selected Columns / Sequences / Region
 275                                                 or everything but the selected Region.</em>
 276                                 </li>
 277                                 <li><strong>Automatic Scrolling<br> </strong><em>When
 278                                                 selected, the view will automatically scroll to display the
 279                                                 highlighted sequence position corresponding to the position under
 280                                                 the mouse pointer in a linked alignment or structure view.</em></li>
 281                                 <li><strong>Show Sequence Features</strong><br> <em>Show
 282                                                 or hide sequence features on this alignment.</em>
 283                                 </li>
 284                                 <li><strong><a href="../features/featuresettings.html">Sequence
 285                                                         Feature Settings...</a> </strong><em><br> <em>Opens the
 286                                                         Sequence Feature Settings dialog box to control the colour and
 287                                                         display of sequence features on the alignment, and configure and
 288                                                         retrieve features from DAS annotation servers.</em>
 289                                 </li>
 290                                 <li><strong>Sequence ID Tooltip</strong><em> (application
 291                                                 only) <br>This submenu's options allow the inclusion or
 292                                                 exclusion of non-positional sequence features or database cross
 293                                                 references from the tooltip shown when the mouse hovers over the
 294                                                 sequence ID panel.</em>
 295                                 </li>
 296                                 <li><strong>Alignment Properties...<br /> </strong><em>Displays
 297                                                 some simple statistics computed for the current alignment view and
 298                                                 any named properties defined on the whole alignment.</em>
 299                                 </li>
 300                                 <li><strong><a href="../features/overview.html">Overview
 301                                                         Window</a><br> </strong><em>A scaled version of the alignment will
 302                                                 be displayed in a small window. A red box will indicate the
 303                                                 currently visible area of the alignment. Move the visible region
 304                                                 using the mouse. </em>
 305                                 </li>
 306                         </ul></li>
 307                 <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
 308                         <ul>
 309                           <li><strong>Show Annotations<br> </strong><em>If this
 310                                                 is selected the &quot;Annotation Panel&quot; will be displayed
 311                                                 below the alignment. The default setting is to display the
 312                                                 conservation calculation, quality calculation and consensus values
 313                                                 as bar charts. </em>
 314                           </li>
 315                           <li><strong>Show Alignment Related</strong><em><br>
 316                             Show all annotations that are for the alignment as a whole (for example, Consensus,
 317                             or secondary structure prediction from alignment).</em></li>
 318                           <li><strong>Hide Alignment Related</strong><em><br>
 319                             Hide all annotations that are for the alignment as a whole.</em></li>
 320                           <li><strong>Show Sequence Related</strong><em><br>
 321                             Show all annotations that are for individual sequences.</em></li>
 322                           <li><strong>Hide Sequence Related</strong><em><br>
 323                             Hide all annotations that are for individual sequences.</em></li>
 324                           <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
 325                             or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
 326                           <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
 327                           (and within that, by label).</em></li>
 328                           <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
 329                           (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
 330                           allowing you to make a manual ordering of the annotations.</em></li>
 331                           <li><strong>Autocalculated Annotation<br> </strong><em>Settings
 332                                         for the display of autocalculated annotation.</em>
 333                                         <ul>
 334                                             <li><strong>Show first<br></strong><em>
 335                                               Show autocalculated annotations above sequence-specific annotations.
 336                                               Note this also applies to other annotations for the alignment, for example secondary
 337                                               structure prediction from alignment.</em></li>
 338                                             <li><strong>Show last<br></strong><em>
 339                                               Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
 340                                                 <li><strong>Apply to all groups<br> </strong><em> When
 341                                                         ticked, any modification to the current settings will be applied
 342                                                         to all autocalculated annotation.</em></li>
 343                                                 <li><strong>Show Consensus Histogram<br> </strong><em>
 344                                                         Enable or disable the display of the histogram above the
 345                                                         consensus sequence.</em></li>
 346                                                 <li><strong>Show Consensus Logo<br> </strong><em> Enable
 347                                                         or disable the display of the Consensus Logo above the consensus
 348                                                         sequence.</em></li>
 349                                                 <li><strong>Normalise Consensus Logo<br>
 350                                                 </strong><em>When enabled, scales all logo stacks to the same height,
 351                                                                 making it easier to compare symbol diversity in highly variable
 352                                                                 regions.</em></li>
 353                                                 <li><strong>Group Conservation<br> </strong><em> When
 354                                                         ticked, display a conservation row for all groups (only available
 355                                                         for protein alignments).</em></li>
 356                                                 <li><strong>Group Consensus<br> </strong><em> When
 357                                                         ticked, display a consensus row for all groups.</em></li>
 358                                         </ul>
 359                                 </li>
 360                         </ul>
 361                 </li>
 362                 <li><strong>Alignment Window Format Menu</strong>
 363                         <ul>
 364                                 <li><strong>Font...<br> </strong><em>Opens the
 365                                                 &quot;Choose Font&quot; dialog box, in order to change the font of
 366                                                 the display and enable or disable 'smooth fonts' (anti-aliasing)
 367                                                 for faster alignment rendering. </em></li>
 368                                 <li><strong>Wrap<br> </strong><em>When ticked, the
 369                                                 alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot;
 370                                                 to the width of the alignment window. This is useful if your
 371                                                 alignment has only a few sequences to view its full width at once.</em><br>
 372                                         Additional options for display of sequence numbering and scales are
 373                                         also visible in wrapped layout mode:<br>
 374                                         <ul>
 375                                                 <li><strong>Scale Above</strong><br><em> Show the alignment
 376                                                         column position scale.</em></li>
 377                                                 <li><strong>Scale Left</strong><br><em> Show the sequence
 378                                                         position for the first aligned residue in each row in the left
 379                                                         column of the alignment.</em></li>
 380                                                 <li><strong>Scale Right</strong><br><em> Show the sequence
 381                                                         position for the last aligned residue in each row in the
 382                                                         right-most column of the alignment.</em></li>
 383                                                 <li><strong>Show Sequence Limits<br> </strong><em>If
 384                                                                 this box is selected the sequence name will have the start and
 385                                                                 end position of the sequence appended to the name, in the format
 386                                                                 NAME/START-END</em>
 387                                                 </li>
 388                                                 <li><strong>Right Align Sequence ID<br> </strong><em>If
 389                                                                 this box is selected then the sequence names displayed in the
 390                                                                 sequence label area will be aligned against the left-hand edge
 391                                                                 of the alignment display, rather than the left-hand edge of the
 392                                                                 alignment window.
 393                                                 </li>
 394                                                 <li><strong>Show Hidden Markers<br> </strong><em>When
 395                                                                 this box is selected, positions in the alignment where rows and
 396                                                                 columns are hidden will be marked by blue arrows.
 397                                                 </li>
 398                                                 <li><strong>Boxes</strong><em><br> If this is
 399                                                                 selected the background of a residue will be coloured using the
 400                                                                 selected background colour. Useful if used in conjunction with
 401                                                                 &quot;Colour Text.&quot; </em>
 402                                                 </li>
 403                                                 <li><strong>Text<br> </strong><em>If this is
 404                                                                 selected the residues will be displayed using the standard 1
 405                                                                 character amino acid alphabet.</em>
 406                                                 </li>
 407                                                 <li><strong>Colour Text<br> </strong><em>If this is
 408                                                                 selected the residues will be coloured according to the
 409                                                                 background colour associated with that residue. The colour is
 410                                                                 slightly darker than background so the amino acid symbol remains
 411                                                                 visible. </em>
 412                                                 </li>
 413                                                 <li><strong>Show Gaps<br> </strong><em>When this is
 414                                                                 selected, gap characters will be displayed as &quot;.&quot; or
 415                                                                 &quot;-&quot;. If unselected, then gap characters will appear as
 416                                                                 blank spaces. <br> You may set the default gap character in
 417                                                                 <a href="../features/preferences.html">preferences</a>.</em>
 418                                                 </li>
 419                                                 <li><strong>Centre Annotation Labels<br> </strong><em>Select
 420                                                                 this to center labels along an annotation row relative to their
 421                                                                 associated column (default is off, i.e. left-justified).</em>
 422                                                 </li>
 423                                                 <li><strong>Show Unconserved<br> </strong><em>When
 424                                                                 this is selected, all consensus sequence symbols will be
 425                                                                 rendered as a '.', highlighting mutations in highly conserved
 426                                                                 alignments. </em>
 427                                                 </li>
 428
 429                                         </ul></li>
 430                         </ul>
 431         </li>
 432
 433                 </ul>
 434                 </li>
 435
 436                 <li><strong>Colour</strong>
 437                         <ul>
 438                                 <li><strong>Apply Colour To All Groups<br> </strong><em>If
 439                                                 this is selected, any changes made to the background colour will
 440                                                 be applied to all currently defined groups.<br> </em>
 441                                 </li>
 442                                 <li><strong><a href="../colourSchemes/textcolour.html">Colour
 443                                                         Text...</a> </strong><em><br> Opens the Colour Text dialog box to
 444                                                 set a different text colour for light and dark background, and the
 445                                                 intensity threshold for transition between them. </em>
 446                                 </li>
 447                                 <li>Colour Scheme options: <strong>None, ClustalX,
 448                                                 Blosum62 Score, Percentage Identity, Zappo, Taylor,
 449                                                 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
 450                                                 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
 451                                                 <a href="../colourSchemes/index.html">colours</a> for a
 452                                                 description of all colour schemes.</em><br></li>
 453                                 <li><strong>By Conservation<br> </strong><em>See <a
 454                                                 href="../colourSchemes/conservation.html">Colouring by
 455                                                         Conservation</a>.</em><br></li>
 456                                 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
 457                                                 this to display the conservation threshold slider window. Useful
 458                                                 if the window has been closed, or if the 'by conservation' option
 459                                                 appears to be doing nothing!</em><br></li>
 460                                 <li><strong>Above Identity Threshold<br> </strong><em>See
 461                                                 <a href="../colourSchemes/abovePID.html">Above Percentage
 462                                                         Identity</a> </em><strong>.<br> </strong>
 463                                 </li>
 464                                 <li><strong>Modify Identity Threshold<br> </strong><em>Use
 465                                                 this to set the threshold value for colouring above Identity.
 466                                                 Useful if the window has been closed.<br> </em>
 467                                 </li>
 468                                 <li><strong>By Annotation</strong><br> <em>Colours
 469                                                 the alignment on a per-column value from a specified annotation.
 470                                                 See <a href="../colourSchemes/annotationColouring.html">Annotation
 471                                                         Colouring</a>.</em><br></li>
 472                 <li><strong>By RNA Helices</strong><br>
 473                 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
 474                 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
 475                 Colouring</a>.</em><br>
 476                 </li>
 477                         </ul></li>
 478                 <li><strong>Calculate</strong>
 479                         <ul>
 480                                 <li><strong>Sort </strong>
 481                                         <ul>
 482                                                 <li><strong>by ID</strong><em><br> This will sort
 483                                                                 the sequences according to sequence name. If the sort is
 484                                                                 repeated, the order of the sorted sequences will be inverted. </em>
 485                                                 </li>
 486                                                 <li><strong>by Length</strong><em><br> This will
 487                                                                 sort the sequences according to their length (excluding gap
 488                                                                 characters). If the sort is repeated, the order of the sorted
 489                                                                 sequences will be inverted. </em></li>
 490                                                 <li><strong>by Group</strong><strong><br> </strong><em>This
 491                                                                 will sort the sequences according to sequence name. If the sort
 492                                                                 is repeated, the order of the sorted sequences will be inverted.
 493                                                 </em><strong></strong></li>
 494                                                 <li><strong>by Pairwise Identity<br> </strong><em>This
 495                                                                 will sort the selected sequences by their percentage identity to
 496                                                                 the consensus sequence. The most similar sequence is put at the
 497                                                                 top. </em></li>
 498                                                 <li><em>The <a href="../calculations/sorting.html">Sort
 499                                                                         menu</a> will have some additional options if you have just done a
 500                                                                 multiple alignment calculation, or opened a tree viewer window.</em><br>
 501                                                 </li>
 502                                         </ul>
 503                                 </li>
 504                                 <li><strong>Calculate Tree </strong> <br> <em>Functions
 505                                                 for calculating trees on the alignment or the currently selected
 506                                                 region. See <a href="../calculations/tree.html">calculating
 507                                                         trees</a>.</em>
 508                                         <ul>
 509                                                 <li><strong>Average Distance Using % Identity</strong></li>
 510                                                 <li><strong>Neighbour Joining Using % Identity</strong></li>
 511                                                 <li><strong>Average Distance Using Blosum62</strong></li>
 512                                                 <li><strong>Neighbour Joining Using Blosum62<br>
 513                                                 </strong></li>
 514                                         </ul>
 515                                         <strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
 516                                 </li>
 517                                 <li><strong>Pairwise Alignments</strong><br> <em>Applies
 518                                                 Smith and Waterman algorithm to selected sequences. See <a
 519                                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
 520                                 </li>
 521                                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
 522                                                 a spatial clustering of the sequences based on similarity scores calculated with
 523                                                 the alignment. See <a href="../calculations/pca.html">Principal
 524                                                         Component Analysis</a>.</em> <br>
 525                                 </li>
 526                                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
 527                                                 option is only visible if Jalview detects one or more white-space
 528                                                 separated values in the description line of the alignment
 529                                                 sequences.<br> When selected, these numbers are parsed into
 530                                                 sequence associated annotation which can then be used to sort the
 531                                                 alignment via the Sort by&#8594;Score menu.</em> <br>
 532                                 </li>
 533                                 <li><strong>Autocalculate Consensus</strong><br> <em>For
 534                                                 large alignments it can be useful to deselect &quot;Autocalculate
 535                                                 Consensus&quot; when editing. This prevents the sometimes lengthy
 536                                                 calculations performed after each sequence edit.</em> <br>
 537                                 </li>
 538                                 <li><strong>Sort With New Tree</strong><br> <em>When
 539                                                 enabled, Jalview will automatically sort the alignment when a new
 540                                                 tree is calculated or loaded onto it.</em> <br></li>
 541                         <li><strong>Show Flanking Regions</strong><br> <em>Opens
 542                                         a new alignment window showing any additional sequence data either
 543                                         side of the current alignment. Useful in conjunction with 'Fetch
 544                                         Database References' when the 'Trim Retrieved Sequences' option is
 545                                         disabled to retrieve full length sequences for a set of aligned
 546                                         peptides. </em></li>
 547                 </ul></li>
 548
 549                 <li><strong>Web Service Menu</strong><br /> <em>This menu
 550                                 is dynamic, and may contain user-defined web service entries in
 551                                 addition to any of the following ones:</em>
 552                         <ul>
 553                                 <li><strong>Fetch DB References</strong><br> <em>This
 554         submenu contains options for accessing any of the database services
 555         that Jalview is aware of (e.g. DAS sequence servers and the
 556         WSDBFetch service provided by the EBI) to verify sequence start/end
 557         positions and retrieve all database cross references and PDB ids
 558         associated with all or just the selected sequences in the alignment.
 559         <ul>
 560           <li>'Trim Retrieved Sequences' - when checked, Jalview will
 561             discard any additional sequence data for accessions associated with
 562             sequences in the alignment. <br> <strong>Note: Disabling this
 563               could cause out of memory errors when working with genomic
 564               sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
 565         </li>
 566           <li>'Standard Databases' will check sequences against the EBI
 567             databases plus any active DAS sequence sources<</li>
 568         </ul> Other sub-menus allow you to pick a specific source to query -
 569         sources are listed alphabetically according to their nickname.
 570     </em><br></li>
 571                         </ul>
 572                         <p>Selecting items from the following submenus will start a
 573                                 remote service on compute facilities at the University of Dundee, or
 574                                 elsewhere. You need a continuous network connection in order to use
 575                                 these services through Jalview.
 576                         </p>
 577                         <ul>
 578                                 <li><strong>Alignment</strong><br /><em> Align the currently
 579                                         selected sequences or all sequences in the alignment, or re-align
 580                                         unaligned sequences to the aligned sequences. Entries in this menu
 581                                         provide access to the various alignment programs supported by <a
 582                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
 583                                         href="../webServices/msaclient.html">Multiple Sequence
 584                                                 Alignment webservice client</a> entry for more information.</em></li>
 585                                 <li><strong>Secondary Structure Prediction</strong>
 586                                         <ul>
 587                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
 588                                                         <em>Secondary structure prediction by network consensus. See
 589                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
 590                                                                 more information. The behaviour of this calculation depends on
 591                                                                 the current selection:
 592                                                                 <ul>
 593                                                                         <li>If nothing is selected, and the displayed sequences
 594                                                                                 appear to be aligned, then a JNet prediction will be run for
 595                                                                                 the first sequence in the alignment, using the current
 596                                                                                 alignment. Otherwise the first sequence will be submitted for
 597                                                                                 prediction.</li>
 598                                                                         <li>If just one sequence (or a region on one sequence) has
 599                                                                                 been selected, it will be submitted to the automatic JNet
 600                                                                                 prediction server for homolog detection and prediction.</li>
 601                                                                         <li>If a set of sequences are selected, and they appear to
 602                                                                                 be aligned, then the alignment will be used for a Jnet
 603                                                                                 prediction on the <strong>first</strong> sequence in the set
 604                                                                                 (that is, the one that appears first in the alignment window).
 605                                                                         </li>
 606                                                                 </ul> </em>
 607                                         </ul></li>
 608                                 <li><strong>Analysis</strong><br />
 609                                         <ul>
 610                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
 611                                                                 functional residue analysis on a protein family alignment with
 612                                                                 sub-families defined on it. See the <a
 613                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
 614                                                                 information.</em>
 615                                                 </li>
 616                                         </ul></li>
 617                         </ul></li>
 618         </ul>
 619
 620 </body>
 621 </html>