help/html/menus/alignmentMenu.html

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  22 <head>
  23 <title>Alignment Window Menus</title>
  24 </head>
  25
  26 <body>
  27   <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE!  -->
  28   <p>
  29     <strong>Alignment Window Menus</strong>
  30   </p>
  31   <ul>
  32                 <li><strong>File</strong>
  33                         <ul>
  34                                 <li><strong>Fetch Sequence</strong><br> <em>Shows a
  35                                                 dialog window in which you can retrieve known ids from Uniprot,
  36                                                 EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
  37                                                 European Bioinformatics Institute. See <a
  38                                                 href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
  39                                 <li><strong>Add Sequences</strong><em><br> Add
  40                                                 sequences to the visible alignment from file, URL, or cut &amp;
  41                                                 paste window </em>
  42                                 </li>
  43                                 <li><strong>Reload</strong><em><br> Reloads the
  44                                                 alignment from the original file, if available.<br> <strong>Warning:
  45                                                         This will delete any edits, analyses and colourings applied since
  46                                                         the alignment was last saved, and cannot be undone.</strong> </em>
  47                                 </li>
  48                                 <li><strong>Save (Control S)</strong><em><br> Saves
  49                                                 the alignment to the file it was loaded from (if available), in
  50                                                 the same format, updating the original in place. </em>
  51                                 </li>
  52                                 <li><strong>Save As (Control Shift S)<br> </strong><em>Save
  53                                                 the alignment to local file. A file selection window will open,
  54                                                 use the &quot;Files of type:&quot; selection box to determine
  55                                                 which <a href="../io/index.html">alignment format</a> to save as.</em>
  56                                 </li>
  57                                 <li><strong>Output to Textbox<br> </strong><em>The
  58                                                 alignment will be displayed in plain text in a new window, which
  59                                                 you can &quot;Copy and Paste&quot; using the pull down menu, or
  60                                                 your standard operating system copy and paste keys. The output
  61                                                 window also has a <strong>&quot;New Window&quot;</strong> button
  62                                                 to import the (possibly edited) text as a new alignment.<br>
  63                                                 Select the format of the text by selecting one of the following
  64                                                 menu items.</em>
  65                                         <ul>
  66                                                 <li><strong>FASTA</strong> </li>
  67                                                 <li><strong>MSF</strong></li>
  68                                                 <li><strong>CLUSTAL</strong></li>
  69                                                 <li><strong>BLC</strong></li>
  70                                                 <li><strong>PIR</strong></li>
  71                                                 <li><strong>PFAM</strong></li>
  72                                                 <li><strong>PileUp</strong></li>
  73                                                 <li><strong>AMSA</strong></li>
  74                                                 <li><strong>STH</strong></li>
  75                                                 <li><strong>Phylip</strong></li>
  76                                                 <li><strong>JSON</strong></li>
  77                                         </ul></li>
  78 <li><strong>Page Setup ...</strong><br>
  79         <em>Open the printing system's Page Setup dialog box, to
  80         control page size, layout and orientation.</em></li>
  81         <li><strong>Print (Control P)<br>
  82         </strong><em>Jalview will print the alignment using the current fonts and
  83         colours of your alignment. If the alignment has annotations visible,
  84         these will be printed below the alignment. If the alignment is wrapped
  85         the number of residues per line of your alignment will depend on the
  86         paper width or your alignment window width, whichever is the smaller. </em></li>
  87         <li><strong>Export Image</strong> <em><br>
  88         Creates an alignment graphic with the current view's annotation,
  89         alignment background colours and group colours. If the alignment is <a
  90                 href="../features/wrap.html">wrapped</a>, the output will also be
  91         wrapped and will have the same visible residue width as the open
  92         alignment. </em>
  93         <ul>
  94                 <li><strong>HTML<br>
  95                 </strong><em>Create a <a href="../io/export.html">web page</a> from your
  96                 alignment.</em></li>
  97                 <li><strong>EPS<br>
  98                 </strong><em>Create an <a href="../io/export.html">Encapsulated
  99                 Postscript</a> file from your alignment.</em></li>
 100                 <li><strong>PNG<br>
 101                 </strong><em>Create a <a href="../io/export.html">Portable Network
 102                 Graphics</a> file from your alignment.</em></li>
 103                 <li><strong>SVG<br>
 104                 </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
 105                 <li><strong>BioJS<br>
 106                 </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
 107         </ul>
 108         </li>
 109         <li><strong>Export Features</strong><em><br> All
 110                                                 features visible on the alignment can be saved to file or
 111                                                 displayed in a textbox in either Jalview or GFF format</em>
 112                                 </li>
 113                                 <li><strong>Export Annotations</strong><em><br> All
 114                                                 annotations visible on the alignment can be saved to file or
 115                                                 displayed in a textbox in Jalview annotations format. </em>
 116                                 </li>
 117                                 <li><strong>Load Associated Tree<br> </strong><em>Jalview
 118                                                 can <a href="../calculations/treeviewer.html">view trees</a>
 119                                                  stored in the Newick file format, and associate them with the
 120                                                 alignment. Note: the ids of the tree file and your alignment MUST
 121                                                 be the same.</em></li>
 122                                 <li><strong>Load Features / Annotations<br> </strong><em>Load
 123                                                 files describing precalculated <a
 124                                                 href="../features/featuresFormat.html">sequence features</a> or <a
 125                                                 href="../features/annotationsFormat.html">alignment
 126                                                         annotations</a>.</em></li>
 127                                 <li><strong>Close (Control W)</strong><br> <em>Close
 128                                                 the alignment window. Make sure you have saved your alignment
 129                                                 before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
 130                                                         As</strong> menu.</em>
 131                                 </li>
 132                         </ul></li>
 133                 <li><strong>Edit</strong>
 134                         <ul>
 135                                 <li><strong>Undo (Control Z)</strong><em><br> This
 136                                                 will undo any edits you make to the alignment. This applies to
 137                                                 insertion or deletion of gaps, cutting residues or sequences from
 138                                                 the alignment or pasting sequences to the current alignment or
 139                                                 sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
 140                                                 colour changes, adjustments to group sizes, or changes to the
 141                                                 annotation panel. </em>
 142                                 </li>
 143                                 <li><strong>Redo (Control Y)<br> </strong><em>Any
 144                                                 actions which you undo can be redone using redo. </em>
 145                                 </li>
 146                                 <li><strong>Cut (Control X)<br> </strong><em>This
 147                                                 will make a copy of the currently selected residues before
 148                                                 removing them from your alignment. Click on a sequence name if you
 149                                                 wish to select a whole sequence. <br> Use &lt;CTRL&gt; and X
 150                                                 (&lt;APPLE&gt; and X on MacOSX) to cut.</em>
 151                                 </li>
 152                                 <li><strong>Copy (Control C)</strong><br> <em>Copies
 153                                                 the currently selected residues to the system clipboard - you can
 154                                                 also do this by pressing &lt;CTRL&gt; and C (&lt;APPLE&gt; and C
 155                                                 on MacOSX). <br> If you try to paste the clipboard contents
 156                                                 to a text editor, you will see the format of the copied residues
 157                                                 FASTA.</em></li>
 158                                 <li><strong>Paste </strong>
 159                                         <ul>
 160                                                 <li><strong>To New Alignment (Control Shift V)<br>
 161                                                 </strong><em>A new alignment window will be created from sequences
 162                                                                 previously copied or cut to the system clipboard. <br> Use
 163                                                                 &lt;CTRL&gt; and &lt;SHIFT&gt; and V(&lt;APPLE&gt; and
 164                                                                 &lt;SHIFT;&gt; and and V on MacOSX) to paste.</em>
 165                                                 </li>
 166                                                 <li><strong>Add To This Alignment (Control V)<br>
 167                                                 </strong><em>Copied sequences from another alignment window can be
 168                                                                 added to the current Jalview alignment. </em>
 169                                                 </li>
 170                                         </ul></li>
 171                                 <li><strong>Delete (Backspace)<br> </strong><em>This
 172                                                 will delete the currently selected residues without copying them
 173                                                 to the clipboard. Like the other edit operations, this can be
 174                                                 undone with <strong>Undo</strong>.</em>
 175                                 </li>
 176                                 <li><strong>Remove Left (Control L)<br> </strong><em>If
 177                                                 the alignment has marked columns, the alignment will be trimmed to
 178                                                 the left of the leftmost marked column. To mark a column, mouse
 179                                                 click the scale bar above the alignment. Click again to unmark a
 180                                                 column, or select &quot;Deselect All&quot; to deselect all
 181                                                 columns.</em></li>
 182                                 <li><strong>Remove Right (Control R)<br> </strong><em>If
 183                                                 the alignment has marked columns, the alignment will be trimmed to
 184                                                 the left of the leftmost marked column. To mark a column, mouse
 185                                                 click the scale bar above the alignment. Click again to unmark a
 186                                                 column, or select &quot;Deselect All&quot; to deselect all
 187                                                 columns.</em></li>
 188                                 <li><strong>Remove Empty Columns (Control E)<br>
 189                                 </strong><em>All columns which only contain gap characters
 190                                                 (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You may
 191                                                 set the default gap character in <a
 192                                                 href="../features/preferences.html">preferences</a>. </em>
 193                                 </li>
 194                                 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
 195                                         <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
 196                                                 deleted from the selected area of the alignment. If no selection
 197                                                 is made, ALL the gaps in the alignment will be removed.<br>
 198                                                 You may set the default gap character in <a
 199                                                 href="../features/preferences.html">preferences</a>. </em>
 200                                 </li>
 201                                 <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
 202                                                 this option brings up a window asking you to select a threshold.
 203                                                 If the percentage identity between any two sequences (under the
 204                                                 current alignment) exceeds this value then one of the sequences
 205                                                 (the shorter) is discarded. Press the &quot;Apply&quot; button to
 206                                                 remove redundant sequences. The &quot;Undo&quot; button will undo
 207                                                 the last redundancy deletion.</em>
 208                                 </li>
 209                                 <li><strong>Pad Gaps<br> </strong><em>When selected,
 210                                                 the alignment will be kept at minimal width (so there are no empty
 211                                                 columns before or after the first or last aligned residue) and all
 212                                                 sequences will be padded with gap characters before and
 213                                                 after their terminating residues.<br> This switch is useful
 214                                                 when making a tree using unaligned sequences and when working with
 215                                                 alignment analysis programs which require 'properly aligned
 216                                                 sequences' to be all the same length.<br> You may set the
 217                                                 default for <strong>Pad Gaps</strong> in the <a
 218                                                 href="../features/preferences.html">preferences</a>. </em>
 219                                 </li>
 220                         </ul></li>
 221                 <li><strong>Select</strong>
 222                         <ul>
 223   <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
 224     <em>Opens the Find dialog box to search for residues, sequence name or residue
 225     position within the alignment and create new sequence features from the queries.
 226     </em>
 227   <li><strong>Select All (Control A)</strong><strong><br>
 228     </strong><em>Selects all the sequences and residues in the alignment. <br>
 229     Use &lt;CTRL&gt; and A (&lt;APPLE&gt; and A on a MacOSX) to select all.</em></em></li>
 230         <li><strong>Deselect All (Escape)<br>
 231         </strong><em>Removes the current selection box (red dashed box) from the
 232         alignment window. All selected sequences, residues and marked columns
 233         will be deselected. </em><em> <br>
 234         Use &lt;ESCAPE&gt; to deselect all.</em></li>
 235         <li><strong>Invert Sequence Selection (Control I)<br>
 236         </strong><em>Any sequence ids currently not selected will replace the
 237         current selection. </em></li>
 238         <li><strong>Invert Column Selection (Control Alt I)<br>
 239         </strong><em>Any columns currently not selected will replace the current
 240         column selection. </em></li>
 241         <li><strong>Create Group (Control G)<br></strong>
 242         <em>Create a group containing the currently selected sequences.</em></li>
 243   <li><strong>Remove Group (Shift Control G)<br></strong>
 244   <em>Ungroup the currently selected sequence group.</em></li>
 245                 <li><strong>Make Groups for selection<br /></strong> <em>The
 246                                 currently selected groups of the alignment will be subdivided
 247                                 according to the contents of the currently selected region. <br />Use
 248                                 this to subdivide an alignment based on the different combinations
 249                                 of residues at marked columns.
 250                 </em></li>
 251                 <li><strong>Undefine Groups (Control U)<br>
 252   </strong><em>The alignment will be reset with no defined groups.<br>
 253   <strong>WARNING</strong>: This cannot be undone.</em></li>
 254     <li><strong><a
 255         href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
 256       <em>Select or Hide columns in the alignment according to
 257         secondary structure, labels and values shown in alignment
 258         annotation rows. </em></li>
 259                 </ul></li>
 260                 <li><strong>View</strong>
 261                         <ul>
 262                                 <li><strong>New View (Control T)</strong><em><br>
 263                                                 Creates a new view from the current alignment view. </em>
 264                                 </li>
 265                                 <li><strong>Expand Views (X)</strong><em><br> Display
 266                                                 each view associated with the alignment in its own alignment
 267                                                 window, allowing several views to be displayed simultaneously. </em>
 268                                 </li>
 269                                 <li><strong>Gather Views (G)</strong><em><br> Each
 270                                                 view associated with the alignment will be displayed within its
 271                                                 own tab on the current alignment window. </em>
 272                                 </li>
 273                                 <li><strong>Show&#8594;(all Columns / Sequences /
 274                                                 Sequences and Columns)</strong><em><br> All hidden Columns /
 275                                                 Sequences / Sequences and Columns will be revealed. </em>
 276                                 </li>
 277                                 <li><strong>Hide&#8594;(all Columns / Sequences /
 278                                                 Selected Region / All but Selected Region )</strong><em><br>
 279                                                 Hides the all the currently selected Columns / Sequences / Region
 280                                                 or everything but the selected Region.</em>
 281                                 </li>
 282                                 <li><strong>Automatic Scrolling<br> </strong><em>When
 283                                                 selected, the view will automatically scroll to display the
 284                                                 highlighted sequence position corresponding to the position under
 285                                                 the mouse pointer in a linked alignment or structure view.</em></li>
 286                                 <li><strong>Show Sequence Features</strong><br> <em>Show
 287                                                 or hide sequence features on this alignment.</em>
 288                                 </li>
 289                                 <li><strong><a href="../features/featuresettings.html">Sequence
 290                                                         Feature Settings...</a> </strong><em><br> <em>Opens the
 291                                                         Sequence Feature Settings dialog box to control the colour and
 292                                                         display of sequence features on the alignment, and configure and
 293                                                         retrieve features from DAS annotation servers.</em>
 294                                 </li>
 295                                 <li><strong>Sequence ID Tooltip</strong><em> (application
 296                                                 only) <br>This submenu's options allow the inclusion or
 297                                                 exclusion of non-positional sequence features or database cross
 298                                                 references from the tooltip shown when the mouse hovers over the
 299                                                 sequence ID panel.</em>
 300                                 </li>
 301                                 <li><strong>Alignment Properties...<br /> </strong><em>Displays
 302                                                 some simple statistics computed for the current alignment view and
 303                                                 any named properties defined on the whole alignment.</em>
 304                                 </li>
 305                                 <li><strong><a href="../features/overview.html">Overview
 306                                                         Window</a><br> </strong><em>A scaled version of the alignment will
 307                                                 be displayed in a small window. A red box will indicate the
 308                                                 currently visible area of the alignment. Move the visible region
 309                                                 using the mouse. </em>
 310                                 </li>
 311                         </ul></li>
 312                 <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
 313                         <ul>
 314                           <li><strong>Show Annotations<br> </strong><em>If this
 315                                                 is selected the &quot;Annotation Panel&quot; will be displayed
 316                                                 below the alignment. The default setting is to display the
 317                                                 conservation calculation, quality calculation and consensus values
 318                                                 as bar charts. </em>
 319                           </li>
 320                           <li><strong>Show Alignment Related</strong><em><br>
 321                             Show all annotations that are for the alignment as a whole (for example, Consensus,
 322                             or secondary structure prediction from alignment).</em></li>
 323                           <li><strong>Hide Alignment Related</strong><em><br>
 324                             Hide all annotations that are for the alignment as a whole.</em></li>
 325                           <li><strong>Show Sequence Related</strong><em><br>
 326                             Show all annotations that are for individual sequences.</em></li>
 327                           <li><strong>Hide Sequence Related</strong><em><br>
 328                             Hide all annotations that are for individual sequences.</em></li>
 329                           <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
 330                             or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
 331                           <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
 332                           (and within that, by label).</em></li>
 333                           <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
 334                           (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
 335                           allowing you to make a manual ordering of the annotations.</em></li>
 336                           <li><strong>Autocalculated Annotation<br> </strong><em>Settings
 337                                         for the display of autocalculated annotation.</em>
 338                                         <ul>
 339                                             <li><strong>Show first<br></strong><em>
 340                                               Show autocalculated annotations above sequence-specific annotations.
 341                                               Note this also applies to other annotations for the alignment, for example secondary
 342                                               structure prediction from alignment.</em></li>
 343                                             <li><strong>Show last<br></strong><em>
 344                                               Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
 345                                                 <li><strong>Apply to all groups<br> </strong><em> When
 346                                                         ticked, any modification to the current settings will be applied
 347                                                         to all autocalculated annotation.</em></li>
 348                                                 <li><strong>Show Consensus Histogram<br> </strong><em>
 349                                                         Enable or disable the display of the histogram above the
 350                                                         consensus sequence.</em></li>
 351                                                 <li><strong>Show Consensus Logo<br> </strong><em> Enable
 352                                                         or disable the display of the Consensus Logo above the consensus
 353                                                         sequence.</em></li>
 354                                                 <li><strong>Normalise Consensus Logo<br>
 355                                                 </strong><em>When enabled, scales all logo stacks to the same height,
 356                                                                 making it easier to compare symbol diversity in highly variable
 357                                                                 regions.</em></li>
 358                                                 <li><strong>Group Conservation<br> </strong><em> When
 359                                                         ticked, display a conservation row for all groups (only available
 360                                                         for protein alignments).</em></li>
 361                                                 <li><strong>Group Consensus<br> </strong><em> When
 362                                                         ticked, display a consensus row for all groups.</em></li>
 363                                         </ul>
 364                                 </li>
 365                         </ul>
 366                 </li>
 367                 <li><strong>Alignment Window Format Menu</strong>
 368                         <ul>
 369                                 <li><strong>Font...<br> </strong><em>Opens the
 370                                                 &quot;Choose Font&quot; dialog box, in order to change the font of
 371                                                 the display and enable or disable 'smooth fonts' (anti-aliasing)
 372                                                 for faster alignment rendering. </em></li>
 373                                 <li><strong>Wrap<br> </strong><em>When ticked, the
 374                                                 alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot;
 375                                                 to the width of the alignment window. This is useful if your
 376                                                 alignment has only a few sequences to view its full width at once.</em><br>
 377                                         Additional options for display of sequence numbering and scales are
 378                                         also visible in wrapped layout mode:<br>
 379                                         <ul>
 380                                                 <li><strong>Scale Above</strong><br><em> Show the alignment
 381                                                         column position scale.</em></li>
 382                                                 <li><strong>Scale Left</strong><br><em> Show the sequence
 383                                                         position for the first aligned residue in each row in the left
 384                                                         column of the alignment.</em></li>
 385                                                 <li><strong>Scale Right</strong><br><em> Show the sequence
 386                                                         position for the last aligned residue in each row in the
 387                                                         right-most column of the alignment.</em></li>
 388                                                 <li><strong>Show Sequence Limits<br> </strong><em>If
 389                                                                 this box is selected the sequence name will have the start and
 390                                                                 end position of the sequence appended to the name, in the format
 391                                                                 NAME/START-END</em>
 392                                                 </li>
 393                                                 <li><strong>Right Align Sequence ID<br> </strong><em>If
 394                                                                 this box is selected then the sequence names displayed in the
 395                                                                 sequence label area will be aligned against the left-hand edge
 396                                                                 of the alignment display, rather than the left-hand edge of the
 397                                                                 alignment window.
 398                                                 </li>
 399                                                 <li><strong>Show Hidden Markers<br> </strong><em>When
 400                                                                 this box is selected, positions in the alignment where rows and
 401                                                                 columns are hidden will be marked by blue arrows.
 402                                                 </li>
 403                                                 <li><strong>Boxes</strong><em><br> If this is
 404                                                                 selected the background of a residue will be coloured using the
 405                                                                 selected background colour. Useful if used in conjunction with
 406                                                                 &quot;Colour Text.&quot; </em>
 407                                                 </li>
 408                                                 <li><strong>Text<br> </strong><em>If this is
 409                                                                 selected the residues will be displayed using the standard 1
 410                                                                 character amino acid alphabet.</em>
 411                                                 </li>
 412                                                 <li><strong>Colour Text<br> </strong><em>If this is
 413                                                                 selected the residues will be coloured according to the
 414                                                                 background colour associated with that residue. The colour is
 415                                                                 slightly darker than background so the amino acid symbol remains
 416                                                                 visible. </em>
 417                                                 </li>
 418                                                 <li><strong>Show Gaps<br> </strong><em>When this is
 419                                                                 selected, gap characters will be displayed as &quot;.&quot; or
 420                                                                 &quot;-&quot;. If unselected, then gap characters will appear as
 421                                                                 blank spaces. <br> You may set the default gap character in
 422                                                                 <a href="../features/preferences.html">preferences</a>.</em>
 423                                                 </li>
 424                                                 <li><strong>Centre Annotation Labels<br> </strong><em>Select
 425                                                                 this to center labels along an annotation row relative to their
 426                                                                 associated column (default is off, i.e. left-justified).</em>
 427                                                 </li>
 428                                                 <li><strong>Show Unconserved<br> </strong><em>When
 429                                                                 this is selected, all consensus sequence symbols will be
 430                                                                 rendered as a '.', highlighting mutations in highly conserved
 431                                                                 alignments. </em>
 432                                                 </li>
 433
 434                                         </ul></li>
 435                         </ul>
 436         </li>
 437
 438                 </ul>
 439                 </li>
 440
 441                 <li><strong>Colour</strong>
 442                         <ul>
 443                                 <li><strong>Apply Colour To All Groups<br> </strong><em>If
 444                                                 this is selected, any changes made to the background colour will
 445                                                 be applied to all currently defined groups.<br> </em>
 446                                 </li>
 447                                 <li><strong><a href="../colourSchemes/textcolour.html">Colour
 448                                                         Text...</a> </strong><em><br> Opens the Colour Text dialog box to
 449                                                 set a different text colour for light and dark background, and the
 450                                                 intensity threshold for transition between them. </em>
 451                                 </li>
 452                                 <li>Colour Scheme options: <strong>None, ClustalX,
 453                                                 Blosum62 Score, Percentage Identity, Zappo, Taylor,
 454                                                 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
 455                                                 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
 456                                                 <a href="../colourSchemes/index.html">colours</a> for a
 457                                                 description of all colour schemes.</em><br></li>
 458                                 <li><strong>By Conservation<br> </strong><em>See <a
 459                                                 href="../colourSchemes/conservation.html">Colouring by
 460                                                         Conservation</a>.</em><br></li>
 461                                 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
 462                                                 this to display the conservation threshold slider window. Useful
 463                                                 if the window has been closed, or if the 'by conservation' option
 464                                                 appears to be doing nothing!</em><br></li>
 465                                 <li><strong>Above Identity Threshold<br> </strong><em>See
 466                                                 <a href="../colourSchemes/abovePID.html">Above Percentage
 467                                                         Identity</a> </em><strong>.<br> </strong>
 468                                 </li>
 469                                 <li><strong>Modify Identity Threshold<br> </strong><em>Use
 470                                                 this to set the threshold value for colouring above Identity.
 471                                                 Useful if the window has been closed.<br> </em>
 472                                 </li>
 473                                 <li><strong>By Annotation</strong><br> <em>Colours
 474                                                 the alignment on a per-column value from a specified annotation.
 475                                                 See <a href="../colourSchemes/annotationColouring.html">Annotation
 476                                                         Colouring</a>.</em><br></li>
 477                 <li><strong>By RNA Helices</strong><br>
 478                 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
 479                 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
 480                 Colouring</a>.</em><br>
 481                 </li>
 482                         </ul></li>
 483                 <li><strong>Calculate</strong>
 484                         <ul>
 485                                 <li><strong>Sort </strong>
 486                                         <ul>
 487                                                 <li><strong>by ID</strong><em><br> This will sort
 488                                                                 the sequences according to sequence name. If the sort is
 489                                                                 repeated, the order of the sorted sequences will be inverted. </em>
 490                                                 </li>
 491                                                 <li><strong>by Length</strong><em><br> This will
 492                                                                 sort the sequences according to their length (excluding gap
 493                                                                 characters). If the sort is repeated, the order of the sorted
 494                                                                 sequences will be inverted. </em></li>
 495                                                 <li><strong>by Group</strong><strong><br> </strong><em>This
 496                                                                 will sort the sequences according to sequence name. If the sort
 497                                                                 is repeated, the order of the sorted sequences will be inverted.
 498                                                 </em><strong></strong></li>
 499                                                 <li><strong>by Pairwise Identity<br> </strong><em>This
 500                                                                 will sort the selected sequences by their percentage identity to
 501                                                                 the consensus sequence. The most similar sequence is put at the
 502                                                                 top. </em></li>
 503                                                 <li><em>The <a href="../calculations/sorting.html">Sort
 504                                                                         menu</a> will have some additional options if you have just done a
 505                                                                 multiple alignment calculation, or opened a tree viewer window.</em><br>
 506                                                 </li>
 507                                         </ul>
 508                                 </li>
 509       <li><strong>Calculate Tree </strong> <br> <em>Functions
 510           for calculating trees on the alignment or the currently
 511           selected region. See <a href="../calculations/tree.html">calculating
 512             trees</a>.
 513       </em>
 514         <ul>
 515           <li><strong>Neighbour Joining Using PAM250 </strong></li>
 516           <li><strong>Neighbour Joining Using Sequence
 517               Feature Similarity</strong></li>
 518           <li><strong>Neighbour Joining Using Blosum62 </strong></li>
 519           <li><strong>Neighbour Joining Using % Identity</strong></li>
 520           <li><strong>Average Distance Using PAM250 </strong></li>
 521           <li><strong>Average Distance Using Sequence
 522               Feature Similarity</strong></li>
 523           <li><strong>Average Distance Using Blosum62</strong></li>
 524           <li><strong>Average Distance Using % Identity</strong></li>
 525         </ul> <strong>Note: Since Version 2.8.1, a number of
 526           additional similarity measures for tree calculation are
 527           provided in this menu.</strong></li>
 528                                 <li><strong>Pairwise Alignments</strong><br> <em>Applies
 529                                                 Smith and Waterman algorithm to selected sequences. See <a
 530                                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
 531                                 </li>
 532                                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
 533                                                 a spatial clustering of the sequences based on similarity scores calculated with
 534                                                 the alignment. See <a href="../calculations/pca.html">Principal
 535                                                         Component Analysis</a>.</em> <br>
 536                                 </li>
 537                                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
 538                                                 option is only visible if Jalview detects one or more white-space
 539                                                 separated values in the description line of the alignment
 540                                                 sequences.<br> When selected, these numbers are parsed into
 541                                                 sequence associated annotation which can then be used to sort the
 542                                                 alignment via the Sort by&#8594;Score menu.</em> <br>
 543                                 </li>
 544                                 <li><strong>Autocalculate Consensus</strong><br> <em>For
 545                                                 large alignments it can be useful to deselect &quot;Autocalculate
 546                                                 Consensus&quot; when editing. This prevents the sometimes lengthy
 547                                                 calculations performed after each sequence edit.</em> <br>
 548                                 </li>
 549                                 <li><strong>Sort With New Tree</strong><br> <em>When
 550                                                 enabled, Jalview will automatically sort the alignment when a new
 551                                                 tree is calculated or loaded onto it.</em> <br></li>
 552                         <li><strong>Show Flanking Regions</strong><br> <em>Opens
 553                                         a new alignment window showing any additional sequence data either
 554                                         side of the current alignment. Useful in conjunction with 'Fetch
 555                                         Database References' when the 'Trim Retrieved Sequences' option is
 556                                         disabled to retrieve full length sequences for a set of aligned
 557                                         peptides. </em></li>
 558                 </ul></li>
 559
 560                 <li><strong>Web Service Menu</strong><br /> <em>This menu
 561                                 is dynamic, and may contain user-defined web service entries in
 562                                 addition to any of the following ones:</em>
 563                         <ul>
 564                                 <li><strong>Fetch DB References</strong><br> <em>This
 565         submenu contains options for accessing any of the database services
 566         that Jalview is aware of (e.g. DAS sequence servers and the
 567         WSDBFetch service provided by the EBI) to verify sequence start/end
 568         positions and retrieve all database cross references and PDB ids
 569         associated with all or just the selected sequences in the alignment.
 570         <ul>
 571           <li>'Trim Retrieved Sequences' - when checked, Jalview will
 572             discard any additional sequence data for accessions associated with
 573             sequences in the alignment. <br> <strong>Note: Disabling this
 574               could cause out of memory errors when working with genomic
 575               sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
 576         </li>
 577           <li>'Standard Databases' will check sequences against the EBI
 578             databases plus any active DAS sequence sources<</li>
 579         </ul> Other sub-menus allow you to pick a specific source to query -
 580         sources are listed alphabetically according to their nickname.
 581     </em><br></li>
 582                         </ul>
 583                         <p>Selecting items from the following submenus will start a
 584                                 remote service on compute facilities at the University of Dundee, or
 585                                 elsewhere. You need a continuous network connection in order to use
 586                                 these services through Jalview.
 587                         </p>
 588                         <ul>
 589                                 <li><strong>Alignment</strong><br /><em> Align the currently
 590                                         selected sequences or all sequences in the alignment, or re-align
 591                                         unaligned sequences to the aligned sequences. Entries in this menu
 592                                         provide access to the various alignment programs supported by <a
 593                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
 594                                         href="../webServices/msaclient.html">Multiple Sequence
 595                                                 Alignment webservice client</a> entry for more information.</em></li>
 596                                 <li><strong>Secondary Structure Prediction</strong>
 597                                         <ul>
 598                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
 599                                                         <em>Secondary structure prediction by network consensus. See
 600                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
 601                                                                 more information. The behaviour of this calculation depends on
 602                                                                 the current selection:
 603                                                                 <ul>
 604                                                                         <li>If nothing is selected, and the displayed sequences
 605                                                                                 appear to be aligned, then a JNet prediction will be run for
 606                                                                                 the first sequence in the alignment, using the current
 607                                                                                 alignment. Otherwise the first sequence will be submitted for
 608                                                                                 prediction.</li>
 609                                                                         <li>If just one sequence (or a region on one sequence) has
 610                                                                                 been selected, it will be submitted to the automatic JNet
 611                                                                                 prediction server for homolog detection and prediction.</li>
 612                                                                         <li>If a set of sequences are selected, and they appear to
 613                                                                                 be aligned, then the alignment will be used for a Jnet
 614                                                                                 prediction on the <strong>first</strong> sequence in the set
 615                                                                                 (that is, the one that appears first in the alignment window).
 616                                                                         </li>
 617                                                                 </ul> </em>
 618                                         </ul></li>
 619                                 <li><strong>Analysis</strong><br />
 620                                         <ul>
 621                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
 622                                                                 functional residue analysis on a protein family alignment with
 623                                                                 sub-families defined on it. See the <a
 624                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
 625                                                                 information.</em>
 626                                                 </li>
 627                                         </ul></li>
 628                         </ul></li>
 629         </ul>
 630
 631 </body>
 632 </html>