help/html/menus/alwcalculate.html

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  19 <head>
  20 <title>Alignment Window Menus</title>
  21 </head>
  22
  23 <body>
  24         <p>
  25                 <strong>Alignment Window Calculate Menu</strong>
  26         </p>
  27         <ul>
  28                 <li><strong>Sort </strong>
  29                         <ul>
  30                                 <li><strong>by ID</strong><em><br> This will sort the
  31                                                 sequences according to sequence name. If the sort is repeated, the
  32                                                 order of the sorted sequences will be inverted. </em>
  33                                 </li>
  34                                 <li><strong>by Length</strong><em><br> This will sort
  35                                                 the sequences according to their length (excluding gap
  36                                                 characters). If the sort is repeated, the order of the sorted
  37                                                 sequences will be inverted. </em>
  38                                 </li>
  39                                 <li><strong>by Group</strong><strong><br> </strong><em>This
  40                                                 will sort the sequences according to sequence name. If the sort is
  41                                                 repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
  42                                 </li>
  43                                 <li><strong>by Pairwise Identity<br> </strong><em>This
  44                                                 will sort the selected sequences by their percentage identity to
  45                                                 the consensus sequence. The most similar sequence is put at the
  46                                                 top. </em>
  47                                 </li>
  48                                 <li><em>The <a href="../calculations/sorting.html">Sort
  49                                                         menu</a> will have some additional options if the alignment has any
  50                                                 associated score annotation, or you have just done a multiple
  51                                                 alignment calculation or opened a tree viewer window.</em><br></li>
  52                         </ul></li>
  53                 <li><strong>Calculate Tree </strong> <br> <em>Functions
  54                                 for calculating trees on the alignment or the currently selected
  55                                 region. See <a href="../calculations/tree.html">calculating
  56                                         trees</a>.</em>
  57                         <ul>
  58                                 <li><strong>Average Distance Using % Identity</strong>
  59                                 </li>
  60                                 <li><strong>Neighbour Joining Using % Identity</strong>
  61                                 </li>
  62                                 <li><strong>Average Distance Using Blosum62</strong>
  63                                 </li>
  64                                 <li><strong>Neighbour Joining Using Blosum62<br>
  65                                 </strong>
  66                                 </li>
  67                         </ul></li>
  68                 <li><strong>Pairwise Alignments</strong><br> <em>Applies
  69                                 Smith and Waterman algorithm to selected sequences. See <a
  70                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
  71                 </li>
  72                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
  73                                 a spatial clustering of the sequences based on the BLOSUM62 scores
  74                                 in the alignment. See <a href="../calculations/pca.html">Principal
  75                                         Component Analysis</a>.</em> <br></li>
  76                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
  77                                 option is only visible if Jalview detects one or more white-space
  78                                 separated values in the description line of the alignment sequences.<br>
  79                                 When selected, these numbers are parsed into sequence associated
  80                                 annotation which can then be used to sort the alignment via the Sort
  81                                 by&#8594;Score menu.</em> <br></li>
  82
  83                 <li><strong>Autocalculate Consensus</strong><br> <em>For
  84                                 large alignments it can be useful to deselect &quot;Autocalculate
  85                                 Consensus&quot; when editing. This prevents the sometimes lengthy
  86                                 calculations performed after each sequence edit.</em> <br></li>
  87                 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
  88                                 this option is selected, the alignment will be automatically sorted
  89                                 whenever a new tree is calculated or loaded.</em> <br>
  90                 </li>
  91         </ul>
  92 </body>
  93 </html>