help/html/menus/alignmentMenu.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <head>
  20 <title>Alignment Window Menus</title>
  21 </head>
  22
  23 <body>
  24         <p>
  25                 <strong>Alignment Window Menus</strong>
  26         </p>
  27         <ul>
  28                 <li><strong>File</strong>
  29                         <ul>
  30                                 <li><strong>Fetch Sequence</strong><br> <em>Shows a
  31                                                 dialog window in which you can retrieve known ids from Uniprot,
  32                                                 EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
  33                                                 European Bioinformatics Institute. See <a
  34                                                 href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
  35                                 <li><strong>Add Sequences</strong><em><br> Add
  36                                                 sequences to the visible alignment from file, URL, or cut &amp;
  37                                                 paste window </em>
  38                                 </li>
  39                                 <li><strong>Reload</strong><em><br> Reloads the
  40                                                 alignment from the original file, if available.<br> <strong>Warning:
  41                                                         This will delete any edits, analyses and colourings applied since
  42                                                         the alignment was last saved, and cannot be undone.</strong> </em>
  43                                 </li>
  44                                 <li><strong>Save (Control S)</strong><em><br> Saves
  45                                                 the alignment to the file it was loaded from (if available), in
  46                                                 the same format, updating the original in place. </em>
  47                                 </li>
  48                                 <li><strong>Save As (Control Shift S)<br> </strong><em>Save
  49                                                 the alignment to local file. A file selection window will open,
  50                                                 use the &quot;Files of type:&quot; selection box to determine
  51                                                 which <a href="../io/index.html">alignment format</a> to save as.</em>
  52                                 </li>
  53                                 <li><strong>Output to Textbox<br> </strong><em>The
  54                                                 alignment will be displayed in plain text in a new window, which
  55                                                 you can &quot;Copy and Paste&quot; using the pull down menu, or
  56                                                 your standard operating system copy and paste keys. The output
  57                                                 window also has a <strong>&quot;New Window&quot;</strong> button
  58                                                 to import the (possibly edited) text as a new alignment.<br>
  59                                                 Select the format of the text by selecting one of the following
  60                                                 menu items.</em>
  61                                         <ul>
  62                                                 <li><strong>FASTA</strong> <em></em>
  63                                                 </li>
  64                                                 <li><strong>MSF</strong>
  65                                                 </li>
  66                                                 <li><strong>CLUSTAL</strong>
  67                                                 </li>
  68                                                 <li><strong>BLC</strong>
  69                                                 </li>
  70                                                 <li><strong>PIR</strong>
  71                                                 </li>
  72                                                 <li><strong>PFAM</strong>
  73                                                 </li>
  74                                         </ul></li>
  75                                 <li><strong>Print (Control P)<br> </strong><em>Jalview
  76                                                 will print the alignment using the current fonts and colours of
  77                                                 your alignment. If the alignment has annotations visible, these
  78                                                 will be printed below the alignment. If the alignment is wrapped
  79                                                 the number of residues per line of your alignment will depend on
  80                                                 the paper width or your alignment window width, whichever is the
  81                                                 smaller. </em>
  82                                 </li>
  83                                 <li><strong>Export Image</strong> <em><br> Creates an
  84                                                 alignment graphic with the current view's annotation, alignment
  85                                                 background colours and group colours. If the alignment is <a
  86                                                 href="../features/wrap.html">wrapped</a>, the output will also be
  87                                                 wrapped and will have the same visible residue width as the open
  88                                                 alignment. </em>
  89                                         <ul>
  90                                                 <li><strong>HTML<br> </strong><em>Create a <a
  91                                                                 href="../io/export.html">web page</a> from your alignment.</em>
  92                                                 </li>
  93                                                 <li><strong>EPS<br> </strong><em>Create an <a
  94                                                                 href="../io/export.html">Encapsulated Postscript</a> file from
  95                                                                 your alignment.</em>
  96                                                 </li>
  97                                                 <li><strong>PNG<br> </strong><em>Create a <a
  98                                                                 href="../io/export.html">Portable Network Graphics</a> file from
  99                                                                 your alignment.</em>
 100                                                 </li>
 101                                         </ul></li>
 102                                 <li><strong>Export Features</strong><em><br> All
 103                                                 features visible on the alignment can be saved to file or
 104                                                 displayed in a textbox in either Jalview or GFF format</em>
 105                                 </li>
 106                                 <li><strong>Export Annotations</strong><em><br> All
 107                                                 annotations visible on the alignment can be saved to file or
 108                                                 displayed in a textbox in Jalview annotations format. </em>
 109                                 </li>
 110                                 <li><strong>Load Associated Tree<br> </strong><em>Jalview
 111                                                 can <a href="../calculations/treeviewer.html">view trees</a>
 112                                                 stored in the Newick file format, and associate them with the
 113                                                 alignment. Note: the ids of the tree file and your alignment MUST
 114                                                 be the same.</em></li>
 115                                 <li><strong>Load Features / Annotations<br> </strong><em>Load
 116                                                 files describing precalculated <a
 117                                                 href="../features/featuresFormat.html">sequence features</a> or <a
 118                                                 href="../features/annotationsFormat.html">alignment
 119                                                         annotations</a>.</em></li>
 120                                 <li><strong>Close (Control W)</strong><br> <em>Close
 121                                                 the alignment window. Make sure you have saved your alignment
 122                                                 before you close - either as a Jalview project or by using the <strong>Save
 123                                                         As</strong> menu.</em>
 124                                 </li>
 125                         </ul></li>
 126                 <li><strong>Edit</strong>
 127                         <ul>
 128                                 <li><strong>Undo (Control Z)</strong><em><br> This
 129                                                 will undo any edits you make to the alignment. This applies to
 130                                                 insertion or deletion of gaps, cutting residues or sequences from
 131                                                 the alignment or pasting sequences to the current alignment or
 132                                                 sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
 133                                                 colour changes, adjustments to group sizes, or changes to the
 134                                                 annotation panel. </em>
 135                                 </li>
 136                                 <li><strong>Redo (Control Y)<br> </strong><em>Any
 137                                                 actions which you undo can be redone using redo. </em>
 138                                 </li>
 139                                 <li><strong>Cut (Control X)<br> </strong><em>This
 140                                                 will make a copy of the currently selected residues before
 141                                                 removing them from your alignment. Click on a sequence name if you
 142                                                 wish to select a whole sequence. <br> Use &lt;CTRL&gt; and X
 143                                                 (&lt;APPLE&gt; and X on MacOSX) to cut.</em>
 144                                 </li>
 145                                 <li><strong>Copy (Control C)</strong><br> <em>Copies
 146                                                 the currently selected residues to the system clipboard - you can
 147                                                 also do this by pressing &lt;CTRL&gt; and C (&lt;APPLE&gt; and C
 148                                                 on MacOSX). <br> If you try to paste the clipboard contents
 149                                                 to a text editor, you will see the format of the copied residues
 150                                                 FASTA.</em></li>
 151                                 <li><strong>Paste </strong>
 152                                         <ul>
 153                                                 <li><strong>To New Alignment (Control Shift V)<br>
 154                                                 </strong><em>A new alignment window will be created from sequences
 155                                                                 previously copied or cut to the system clipboard. <br> Use
 156                                                                 &lt;CTRL&gt; and &lt;SHIFT&gt; and V(&lt;APPLE&gt; and
 157                                                                 &lt;SHIFT;&gt; and and V on MacOSX) to paste.</em>
 158                                                 </li>
 159                                                 <li><strong>Add To This Alignment (Control V)<br>
 160                                                 </strong><em>Copied sequences from another alignment window can be
 161                                                                 added to the current Jalview alignment. </em>
 162                                                 </li>
 163                                         </ul></li>
 164                                 <li><strong>Delete (Backspace)<br> </strong><em>This
 165                                                 will delete the currently selected residues without copying them
 166                                                 to the clipboard. Like the other edit operations, this can be
 167                                                 undone with <strong>Undo</strong>.</em>
 168                                 </li>
 169                                 <li><strong>Remove Left (Control L)<br> </strong><em>If
 170                                                 the alignment has marked columns, the alignment will be trimmed to
 171                                                 the left of the leftmost marked column. To mark a column, mouse
 172                                                 click the scale bar above the alignment. Click again to unmark a
 173                                                 column, or select &quot;Deselect All&quot; to deselect all
 174                                                 columns.</em></li>
 175                                 <li><strong>Remove Right (Control R)<br> </strong><em>If
 176                                                 the alignment has marked columns, the alignment will be trimmed to
 177                                                 the left of the leftmost marked column. To mark a column, mouse
 178                                                 click the scale bar above the alignment. Click again to unmark a
 179                                                 column, or select &quot;Deselect All&quot; to deselect all
 180                                                 columns.</em></li>
 181                                 <li><strong>Remove Empty Columns (Control E)<br>
 182                                 </strong><em>All columns which only contain gap characters
 183                                                 (&quot;-&quot;, &quot;.&quot;) will be deleted.<br> You may
 184                                                 set the default gap character in <a
 185                                                 href="../features/preferences.html">preferences</a>. </em>
 186                                 </li>
 187                                 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
 188                                         <em>Gap characters (&quot;-&quot;, &quot;.&quot;) will be
 189                                                 deleted from the selected area of the alignment. If no selection
 190                                                 is made, ALL the gaps in the alignment will be removed.<br>
 191                                                 You may set the default gap character in <a
 192                                                 href="../features/preferences.html">preferences</a>. </em>
 193                                 </li>
 194                                 <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
 195                                                 this option brings up a window asking you to select a threshold.
 196                                                 If the percentage identity between any two sequences (under the
 197                                                 current alignment) exceeds this value then one of the sequences
 198                                                 (the shorter) is discarded. Press the &quot;Apply&quot; button to
 199                                                 remove redundant sequences. The &quot;Undo&quot; button will undo
 200                                                 the last redundancy deletion.</em>
 201                                 </li>
 202                                 <li><strong>Pad Gaps<br> </strong><em>When selected,
 203                                                 the alignment will be kept at minimal width (so there no empty
 204                                                 columns before or after the first or last aligned residue) and all
 205                                                 sequences will be padded with gap characters to the before and
 206                                                 after their terminating residues.<br> This switch is useful
 207                                                 when making a tree using unaligned sequences and when working with
 208                                                 alignment analysis programs which require 'properly aligned
 209                                                 sequences' to be all the same length.<br> You may set the
 210                                                 default for <strong>Pad Gaps</strong> in the <a
 211                                                 href="../features/preferences.html">preferences</a>. </em>
 212                                 </li>
 213                         </ul></li>
 214                 <li><strong>Select</strong>
 215                         <ul>
 216                                 <li><strong><a href="../features/search.html">Find...
 217                                                         (Control F)</a> </strong><em><br> Opens the Find dialog box to
 218                                                 search for residues, sequence name or residue position within the
 219                                                 alignment and create new sequence features from the queries. </em>
 220                                 </li>
 221                                 <li><strong>Select All (Control A)<br> </strong><em>Selects
 222                                                 all the sequences and residues in the alignment. <br> Use
 223                                                 &lt;CTRL&gt; and A (&lt;APPLE&gt; and A on a MacOSX) to select
 224                                                 all.</em></li>
 225                                 <li><strong>Deselect All (Escape)<br> </strong><em>Removes
 226                                                 the current selection box (red dashed box) from the alignment
 227                                                 window. All selected sequences, residues and marked columns will
 228                                                 be deselected. </em><em> <br> Use &lt;ESCAPE&gt; to deselect
 229                                                 all.</em></li>
 230                                 <li><strong>Invert Sequence Selection (Control I)<br>
 231                                 </strong><em>Any sequence ids currently not selected will replace the
 232                                                 current selection. </em>
 233                                 </li>
 234                                 <li><strong>Invert Column Selection (Control Alt I)<br>
 235                                 </strong><em>Any columns currently not selected will replace the current
 236                                                 column selection. </em>
 237                                 </li>
 238                                 <li><strong>Undefine Groups (Control U)<br> </strong><em>The
 239                                                 alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
 240                                                 This cannot be undone.</em>
 241                                 </li>
 242                                 <li><strong>Make Groups<br /> </strong> <em>The currently
 243                                                 selected groups of the alignment will be subdivided according to
 244                                                 the contents of the currently selected region. <br />Use this to
 245                                                 subdivide an alignment based on the different combinations of
 246                                                 residues observed at specific positions. (new in jalview 2.5)</em>
 247                                 </li>
 248                         </ul></li>
 249                 <li><strong>View</strong>
 250                         <ul>
 251                                 <li><strong>New View (Control T)</strong><em><br>
 252                                                 Creates a new view from the current alignment view. </em>
 253                                 </li>
 254                                 <li><strong>Expand Views (X)</strong><em><br> Display
 255                                                 each view associated with the alignment in its own alignment
 256                                                 window, allowing several views to be displayed simultaneously. </em>
 257                                 </li>
 258                                 <li><strong>Gather Views (G)</strong><em><br> Each
 259                                                 view associated with the alignment will be displayed within its
 260                                                 own tab on the current alignment window. </em>
 261                                 </li>
 262                                 <li><strong>Show&#8594;(all Columns / Sequences /
 263                                                 Sequences and Columns)</strong><em><br> All hidden Columns /
 264                                                 Sequences / Sequences and Columns will be revealed. </em>
 265                                 </li>
 266                                 <li><strong>Hide&#8594;(all Columns / Sequences /
 267                                                 Selected Region / All but Selected Region )</strong><em><br>
 268                                                 Hides the all the currently selected Columns / Sequences / Region
 269                                                 or everything but the selected Region.</em>
 270                                 </li>
 271                                 <li><strong>Automatic Scrolling<br> </strong><em>When
 272                                                 selected, the view will automatically scroll to display the
 273                                                 highlighted sequence position corresponding to the position under
 274                                                 the mouse pointer in a linked alignment or structure view.</em></li>
 275                                 <li><strong>Show Annotations<br> </strong><em>If this
 276                                                 is selected the &quot;Annotation Panel&quot; will be displayed
 277                                                 below the alignment. The default setting is to display the
 278                                                 conservation calculation, quality calculation and consensus values
 279                                                 as bar charts. </em>
 280                                 </li>
 281                                 <li><strong>Autocalculated Annotation<br> </strong><em>Settings
 282                                         for the display of autocalculated annotation.</em>
 283                                         <ul>
 284                                                 <li><strong>Apply to all groups<br> </strong><em> When
 285                                                         ticked, any modification to the current settings will be applied
 286                                                         to all autocalculated annotation.</em></li>
 287                                                 <li><strong>Show Consensus Histogram<br> </strong><em>
 288                                                         Enable or disable the display of the histogram above the
 289                                                         consensus sequence.</em></li>
 290                                                 <li><strong>Show Consensus Profile<br> </strong><em> Enable
 291                                                         or disable the display of the sequence logo above the consensus
 292                                                         sequence.</em></li>
 293                                                 <li><strong>Group Conservation<br> </strong><em> When
 294                                                         ticked, display a conservation row for all groups (only available
 295                                                         for protein alignments).</em></li>
 296                                                 <li><strong>Apply to all groups<br> </strong><em> When
 297                                                         ticked, display a consensus row for all groups.</em></li>
 298                                         </ul></li>
 299                                 <li><strong>Show Sequence Features</strong><br> <em>Show
 300                                                 or hide sequence features on this alignment.</em>
 301                                 </li>
 302                                 <li><strong><a href="../features/featuresettings.html">Seqence
 303                                                         Feature Settings...</a> </strong><em><br> <em>Opens the
 304                                                         Sequence Feature Settings dialog box to control the colour and
 305                                                         display of sequence features on the alignment, and configure and
 306                                                         retrieve features from DAS annotation servers.</em>
 307                                 </li>
 308                                 <li><strong>Sequence ID Tooltip</strong><em> (application
 309                                                 only) <br>This submenu's options allow the inclusion or
 310                                                 exclusion of non-positional sequence features or database cross
 311                                                 references from the tooltip shown when the mouse hovers over the
 312                                                 sequence ID panel.</em>
 313                                 </li>
 314                                 <li><strong>Alignment Properties...<br /> </strong><em>Displays
 315                                                 some simple statistics computed for the current alignment view and
 316                                                 any named properties defined on the whole alignment.</em>
 317                                 </li>
 318                                 <li><strong><a href="../features/overview.html">Overview
 319                                                         Window</a><br> </strong><em>A scaled version of the alignment will
 320                                                 be displayed in a small window. A red box will indicate the
 321                                                 currently visible area of the alignment. Move the visible region
 322                                                 using the mouse. </em>
 323                                 </li>
 324                         </ul></li>
 325                 <li><strong>Alignment Window Format Menu</strong>
 326                         <ul>
 327                                 <li><strong>Font...<br> </strong><em>Opens the
 328                                                 &quot;Choose Font&quot; dialog box, in order to change the font of
 329                                                 the display and enable or disable 'smooth fonts' (anti-aliasing)
 330                                                 for faster alignment rendering. </em></li>
 331                                 <li><strong>Wrap<br> </strong><em>When ticked, the
 332                                                 alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot;
 333                                                 to the width of the alignment window. This is useful if your
 334                                                 alignment has only a few sequences to view its full width at once.</em><br>
 335                                         Additional options for display of sequence numbering and scales are
 336                                         also visible in wrapped layout mode:<br>
 337                                         <ul>
 338                                                 <li><strong>Scale Above</strong><br><em> Show the alignment
 339                                                         column position scale.</em></li>
 340                                                 <li><strong>Scale Left</strong><br><em> Show the sequence
 341                                                         position for the first aligned residue in each row in the left
 342                                                         column of the alignment.</em></li>
 343                                                 <li><strong>Scale Right</strong><br><em> Show the sequence
 344                                                         position for the last aligned residue in each row in the
 345                                                         right-most column of the alignment.</em></li>
 346                                                 <li><strong>Show Sequence Limits<br> </strong><em>If
 347                                                                 this box is selected the sequence name will have the start and
 348                                                                 end position of the sequence appended to the name, in the format
 349                                                                 NAME/START-END</em>
 350                                                 </li>
 351                                                 <li><strong>Right Align Sequence ID<br> </strong><em>If
 352                                                                 this box is selected then the sequence names displayed in the
 353                                                                 sequence label area will be aligned against the left-hand edge
 354                                                                 of the alignment display, rather than the left-hand edge of the
 355                                                                 alignment window.
 356                                                 </li>
 357                                                 <li><strong>Show Hidden Markers<br> </strong><em>When
 358                                                                 this box is selected, positions in the alignment where rows and
 359                                                                 columns are hidden will be marked by blue arrows.
 360                                                 </li>
 361                                                 <li><strong>Boxes</strong><em><br> If this is
 362                                                                 selected the background of a residue will be coloured using the
 363                                                                 selected background colour. Useful if used in conjunction with
 364                                                                 &quot;Colour Text.&quot; </em>
 365                                                 </li>
 366                                                 <li><strong>Text<br> </strong><em>If this is
 367                                                                 selected the residues will be displayed using the standard 1
 368                                                                 character amino acid alphabet.</em>
 369                                                 </li>
 370                                                 <li><strong>Colour Text<br> </strong><em>If this is
 371                                                                 selected the residues will be coloured according to the
 372                                                                 background colour associated with that residue. The colour is
 373                                                                 slightly darker than background so the amino acid symbol remains
 374                                                                 visible. </em>
 375                                                 </li>
 376                                                 <li><strong>Show Gaps<br> </strong><em>When this is
 377                                                                 selected, gap characters will be displayed as &quot;.&quot; or
 378                                                                 &quot;-&quot;. If unselected, then gap characters will appear as
 379                                                                 blank spaces. <br> You may set the default gap character in
 380                                                                 <a href="../features/preferences.html">preferences</a>.</em>
 381                                                 </li>
 382                                                 <li><strong>Centre Annotation Labels<br> </strong><em>Select
 383                                                                 this to center labels along an annotation row relative to their
 384                                                                 associated column (default is off, i.e. left-justified).</em>
 385                                                 </li>
 386                                                 <li><strong>Show Unconserved<br> </strong><em>When
 387                                                                 this is selected, all consensus sequence symbols will be
 388                                                                 rendered as a '.', highlighting mutations in highly conserved
 389                                                                 alignments. </em>
 390                                                 </li>
 391
 392                                         </ul></li>
 393                         </ul>
 394         </li>
 395
 396                 </ul>
 397                 </li>
 398
 399                 <li><strong>Colour</strong>
 400                         <ul>
 401                                 <li><strong>Apply Colour To All Groups<br> </strong><em>If
 402                                                 this is selected, any changes made to the background colour will
 403                                                 be applied to all currently defined groups.<br> </em>
 404                                 </li>
 405                                 <li><strong><a href="../colourSchemes/textcolour.html">Colour
 406                                                         Text...</a> </strong><em><br> Opens the Colour Text dialog box to
 407                                                 set a different text colour for light and dark background, and the
 408                                                 intensity threshold for transition between them. </em>
 409                                 </li>
 410                                 <li>Colour Scheme options: <strong>None, ClustalX,
 411                                                 Blosum62 Score, Percentage Identity, Zappo, Taylor,
 412                                                 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
 413                                                 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
 414                                                 <a href="../colourSchemes/index.html">colours</a> for a
 415                                                 description of all colour schemes.</em><br></li>
 416                                 <li><strong>By Conservation<br> </strong><em>See <a
 417                                                 href="../colourSchemes/conservation.html">Colouring by
 418                                                         Conservation</a>.</em><br></li>
 419                                 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
 420                                                 this to display the conservation threshold slider window. Useful
 421                                                 if the window has been closed, or if the 'by conservation' option
 422                                                 appears to be doing nothing!</em><br></li>
 423                                 <li><strong>Above Identity Threshold<br> </strong><em>See
 424                                                 <a href="../colourSchemes/abovePID.html">Above Percentage
 425                                                         Identity</a> </em><strong>.<br> </strong>
 426                                 </li>
 427                                 <li><strong>Modify Identity Threshold<br> </strong><em>Use
 428                                                 this to set the threshold value for colouring above Identity.
 429                                                 Useful if the window has been closed.<br> </em>
 430                                 </li>
 431                                 <li><strong>By Annotation</strong><br> <em>Colours
 432                                                 the alignment on a per-column value from a specified annotation.
 433                                                 See <a href="../colourSchemes/annotationColouring.html">Annotation
 434                                                         Colouring</a>.</em><br></li>
 435                 <li><strong>By RNA Helices</strong><br>
 436                 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
 437                 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
 438                 Colouring</a>.</em><br>
 439                 </li>
 440                         </ul></li>
 441                 <li><strong>Calculate</strong>
 442                         <ul>
 443                                 <li><strong>Sort </strong>
 444                                         <ul>
 445                                                 <li><strong>by ID</strong><em><br> This will sort
 446                                                                 the sequences according to sequence name. If the sort is
 447                                                                 repeated, the order of the sorted sequences will be inverted. </em>
 448                                                 </li>
 449                                                 <li><strong>by Length</strong><em><br> This will
 450                                                                 sort the sequences according to their length (excluding gap
 451                                                                 characters). If the sort is repeated, the order of the sorted
 452                                                                 sequences will be inverted. </em></li>
 453                                                 <li><strong>by Group</strong><strong><br> </strong><em>This
 454                                                                 will sort the sequences according to sequence name. If the sort
 455                                                                 is repeated, the order of the sorted sequences will be inverted.
 456                                                 </em><strong></strong></li>
 457                                                 <li><strong>by Pairwise Identity<br> </strong><em>This
 458                                                                 will sort the selected sequences by their percentage identity to
 459                                                                 the consensus sequence. The most similar sequence is put at the
 460                                                                 top. </em></li>
 461                                                 <li><em>The <a href="../calculations/sorting.html">Sort
 462                                                                         menu</a> will have some additional options if you have just done a
 463                                                                 multiple alignment calculation, or opened a tree viewer window.</em><br>
 464                                                 </li>
 465                                         </ul>
 466                                 </li>
 467                                 <li><strong>Calculate Tree </strong> <br> <em>Functions
 468                                                 for calculating trees on the alignment or the currently selected
 469                                                 region. See <a href="../calculations/tree.html">calculating
 470                                                         trees</a>.</em>
 471                                         <ul>
 472                                                 <li><strong>Average Distance Using % Identity</strong></li>
 473                                                 <li><strong>Neighbour Joining Using % Identity</strong></li>
 474                                                 <li><strong>Average Distance Using Blosum62</strong></li>
 475                                                 <li><strong>Neighbour Joining Using Blosum62<br>
 476                                                 </strong></li>
 477                                         </ul>
 478                                 </li>
 479                                 <li><strong>Pairwise Alignments</strong><br> <em>Applies
 480                                                 Smith and Waterman algorithm to selected sequences. See <a
 481                                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
 482                                 </li>
 483                                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
 484                                                 a spatial clustering of the sequences based on the BLOSUM62 scores
 485                                                 in the alignment. See <a href="../calculations/pca.html">Principal
 486                                                         Component Analysis</a>.</em> <br>
 487                                 </li>
 488                                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
 489                                                 option is only visible if Jalview detects one or more white-space
 490                                                 separated values in the description line of the alignment
 491                                                 sequences.<br> When selected, these numbers are parsed into
 492                                                 sequence associated annotation which can then be used to sort the
 493                                                 alignment via the Sort by&#8594;Score menu.</em> <br>
 494                                 </li>
 495                                 <li><strong>Autocalculate Consensus</strong><br> <em>For
 496                                                 large alignments it can be useful to deselect &quot;Autocalculate
 497                                                 Consensus&quot; when editing. This prevents the sometimes lengthy
 498                                                 calculations performed after each sequence edit.</em> <br>
 499                                 </li>
 500                                 <li><strong>Sort With New Tree</strong><br> <em>When
 501                                                 enabled, Jalview will automatically sort the alignment when a new
 502                                                 tree is calculated or loaded onto it.</em> <br></li>
 503                         </ul></li>
 504
 505                 <li><strong>Web Service Menu</strong><br /> <em>This menu
 506                                 is dynamic, and may contain user-defined web service entries in
 507                                 addition to any of the following ones:</em>
 508                         <ul>
 509                                 <li><strong>Fetch DB References</strong><br> <em>This
 510                                                 will use any of the database services that Jalview is aware of
 511                                                 (e.g. DAS sequence servers and the WSDBFetch service provided by
 512                                                 the EBI) to verify the sequence and retrieve all database cross
 513                                                 references and PDB ids associated with all or just the selected
 514                                                 sequences in the alignment. <br />'Standard Databases' will check
 515                                                 sequences against the EBI databases plus any active DAS sequence
 516                                                 sources, or you can verify against a specific source from one of
 517                                                 the sub-menus.</em><br></li>
 518                                 <li><strong>Envision2 Services</strong><br /><em> Submits one or
 519                                         more sequences, sequence IDs or database references to analysis
 520                                         workflows provided by the <a
 521                                         href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
 522                                                 application</a>. This allows Jalview users to easily access the EnCore
 523                                         network of databases and analysis services developed by members of
 524                                         <a href="http://www.enfin.org">ENFIN</a></em>.</li>
 525                         </ul>
 526                         <p>Selecting items from the following submenus will start a
 527                                 remote service on compute facilities at the University of Dundee, or
 528                                 elsewhere. You need a continuous network connection in order to use
 529                                 these services through Jalview.
 530                         </p>
 531                         <ul>
 532                                 <li><strong>Alignment</strong><br /><em> Align the currently
 533                                         selected sequences or all sequences in the alignment, or re-align
 534                                         unaligned sequences to the aligned sequences. Entries in this menu
 535                                         provide access to the various alignment programs supported by <a
 536                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
 537                                         href="../webServices/msaclient.html">Multiple Sequence
 538                                                 Alignment webservice client</a> entry for more information.</em></li>
 539                                 <li><strong>Secondary Structure Prediction</strong>
 540                                         <ul>
 541                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
 542                                                         <em>Secondary structure prediction by network consensus. See
 543                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
 544                                                                 more information. The behaviour of this calculation depends on
 545                                                                 the current selection:
 546                                                                 <ul>
 547                                                                         <li>If nothing is selected, and the displayed sequences
 548                                                                                 appear to be aligned, then a JNet prediction will be run for
 549                                                                                 the first sequence in the alignment, using the current
 550                                                                                 alignment. Otherwise the first sequence will be submitted for
 551                                                                                 prediction.</li>
 552                                                                         <li>If just one sequence (or a region on one sequence) has
 553                                                                                 been selected, it will be submitted to the automatic JNet
 554                                                                                 prediction server for homolog detection and prediction.</li>
 555                                                                         <li>If a set of sequences are selected, and they appear to
 556                                                                                 be aligned, then the alignment will be used for a Jnet
 557                                                                                 prediction on the <strong>first</strong> sequence in the set
 558                                                                                 (that is, the one that appears first in the alignment window).
 559                                                                         </li>
 560                                                                 </ul> </em>
 561                                         </ul></li>
 562                                 <li><strong>Analysis</strong><br />
 563                                         <ul>
 564                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
 565                                                                 functional residue analysis on a protein family alignment with
 566                                                                 sub-families defined on it. See the <a
 567                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
 568                                                                 information.</em>
 569                                                 </li>
 570                                         </ul></li>
 571                         </ul></li>
 572         </ul>
 573
 574 </body>
 575 </html>