help/html/menus/alwcalculate.html

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  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>.</em>
  60                         <ul>
  61                                 <li><strong>Average Distance Using % Identity</strong>
  62                                 </li>
  63                                 <li><strong>Neighbour Joining Using % Identity</strong>
  64                                 </li>
  65                                 <li><strong>Average Distance Using Blosum62</strong>
  66                                 </li>
  67                                 <li><strong>Neighbour Joining Using Blosum62<br>
  68                                 </strong>
  69                                 </li>
  70                         </ul></li>
  71                 <li><strong>Pairwise Alignments</strong><br> <em>Applies
  72                                 Smith and Waterman algorithm to selected sequences. See <a
  73                                 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
  74                 </li>
  75                 <li><strong>Principal Component Analysis</strong><br> <em>Shows
  76                                 a spatial clustering of the sequences based on the BLOSUM62 scores
  77                                 in the alignment. See <a href="../calculations/pca.html">Principal
  78                                         Component Analysis</a>.</em> <br></li>
  79                 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
  80                                 option is only visible if Jalview detects one or more white-space
  81                                 separated values in the description line of the alignment sequences.<br>
  82                                 When selected, these numbers are parsed into sequence associated
  83                                 annotation which can then be used to sort the alignment via the Sort
  84                                 by&#8594;Score menu.</em> <br></li>
  85                 <li><strong>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
  86                         Selecting this option shows the DNA's calculated protein product in a new window. Note that the
  87                         translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
  88                         standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded).
  89                         You can perform this action on the whole alignment,
  90                         or selected rows, columns, or regions.</em> <br></li>
  91                 <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
  92                         other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
  93                         Select the database to view all cross-referenced sequences in a new window.</em> <br></li>
  94                 <li><strong>Autocalculate Consensus</strong><br> <em>For
  95                                 large alignments it can be useful to deselect &quot;Autocalculate
  96                                 Consensus&quot; when editing. This prevents the sometimes lengthy
  97                                 calculations performed after each sequence edit.</em> <br></li>
  98                 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
  99                                 this option is selected, the alignment will be automatically sorted
 100                                 whenever a new tree is calculated or loaded.</em> <br>
 101                 </li>
 102         </ul>
 103 </body>
 104 </html>