help/html/menus/alwcalculate.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  22 <head>
  23 <title>Alignment Window Menus</title>
  24 </head>
  25
  26 <body>
  27         <p>
  28                 <strong>Alignment Window Calculate Menu</strong>
  29         </p>
  30         <ul>
  31                 <li><strong>Sort </strong>
  32                         <ul>
  33                                 <li><strong>By ID</strong><em><br> This will sort the
  34                                                 sequences according to sequence name. If the sort is repeated, the
  35                                                 order of the sorted sequences will be inverted. </em>
  36                                 </li>
  37                                 <li><strong>By Length</strong><em><br> This will sort
  38                                                 the sequences according to their length (excluding gap
  39                                                 characters). If the sort is repeated, the order of the sorted
  40                                                 sequences will be inverted. </em>
  41                                 </li>
  42                                 <li><strong>By Group</strong><strong><br> </strong><em>This
  43                                                 will sort the sequences according to sequence name. If the sort is
  44                                                 repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
  45                                 </li>
  46                                 <li><strong>By Pairwise Identity<br> </strong><em>This
  47                                                 will sort the selected sequences by their percentage identity to
  48                                                 the consensus sequence. The most similar sequence is put at the
  49                                                 top. </em>
  50                                 </li>
  51                                 <li><em>The <a href="../calculations/sorting.html">Sort
  52                                                         menu</a> will have some additional options if the alignment has any
  53                                                 associated score annotation, or you have just done a multiple
  54                                                 alignment calculation or opened a tree viewer window.</em><br></li>
  55                         </ul></li>
  56     <li><strong>Calculate Tree </strong> <br> <em>Functions
  57         for calculating trees on the alignment or the currently selected
  58         region. See <a href="../calculations/tree.html">calculating
  59           trees</a>.
  60     </em>
  61       <ul>
  62         <li><strong>Neighbour Joining Using PAM250<br>
  63         </strong></li>
  64         <li><strong>Neighbour Joining Using Sequence
  65             Feature Similarity</strong></li>
  66         <li><strong>Neighbour Joining Using Blosum62<br>
  67         </strong></li>
  68         <li><strong>Neighbour Joining Using % Identity</strong></li>
  69         <li><strong>Average Distance Using PAM250<br>
  70         </strong></li>
  71         <li><strong>Average Distance Using Sequence
  72             Feature Similarity</strong></li>
  73         <li><strong>Average Distance Using Blosum62</strong></li>
  74         <li><strong>Average Distance Using % Identity</strong></li>
  75       </ul></li>
  76     <li><strong>Pairwise Alignments</strong><br> <em>Applies
  77                                 Smith and Waterman algorithm to selected sequences. See <a
  78                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
  79                 </li>
  80                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
  81                                 a spatial clustering of the sequences based on similarity scores calculated over the alignment.. See <a href="../calculations/pca.html">Principal
  82                                         Component Analysis</a>.</em> <br></li>
  83                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
  84                                 option is only visible if Jalview detects one or more white-space
  85                                 separated values in the description line of the alignment sequences.<br>
  86                                 When selected, these numbers are parsed into sequence associated
  87                                 annotation which can then be used to sort the alignment via the Sort
  88                                 by&#8594;Score menu.</em> <br></li>
  89                 <li><strong>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
  90                         Selecting this option shows the DNA's calculated protein product in a new <a href="../features/splitView.html">split frame</a> window. Note that the
  91                         translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
  92                         standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded).
  93                         You can perform this action on the whole alignment,
  94                         or selected rows, columns, or regions.</em> <br></li>
  95                 <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
  96                         other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
  97                         Select the database to view all cross-referenced sequences in a new <a href="../features/splitView.html">split frame</a> window.</em> <br></li>
  98                 <li><strong>Autocalculate Consensus</strong><br> <em>For
  99                                 large alignments it can be useful to deselect &quot;Autocalculate
 100                                 Consensus&quot; when editing. This prevents the sometimes lengthy
 101                                 calculations performed after each sequence edit.</em> <br></li>
 102                 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
 103                                 this option is selected, the alignment will be automatically sorted
 104                                 whenever a new tree is calculated or loaded.</em> <br>
 105                 </li>
 106     <li><strong>Show Flanking Regions</strong><br> <em>Opens
 107         a new alignment window showing any additional sequence data
 108         either side of the current alignment. Useful in conjunction with
 109         'Fetch Database References' when the 'Trim Retrieved Sequences'
 110         option is disabled to retrieve full length sequences for a set
 111         of aligned peptides. </em></li>
 112   </ul>
 113 </body>
 114 </html>