2 <head><title>Alignment Window Menus</title></head>
5 <p><strong>Alignment Window Calculate Menu</strong></p>
7 <li><strong>Sort </strong>
9 <li><strong>by ID</strong><em><br>
10 This will sort the sequences according to sequence name. If the sort is
11 repeated, the order of the sorted sequences will be inverted. </em></li>
12 <li><strong>by Group</strong><strong><br>
13 </strong><em>This will sort the sequences according to sequence name.
14 If the sort is repeated, the order of the sorted sequences will be inverted.
15 </em><strong></strong></li>
16 <li><strong>by Pairwise Identity<br>
17 </strong><em>This will sort the selected sequences by their percentage
18 identity to the consensus sequence. The most similar sequence is put at
20 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
21 some additional options if the alignment has any associated
22 score annotation, or you have just done a multiple alignment calculation
23 or opened a tree viewer window.</em><br>
27 <li><strong>Calculate Tree </strong> <br>
28 <em>Functions for calculating trees on the alignment or the currently selected
30 href="../calculations/tree.html">calculating trees</a>.</em>
32 <li><strong>Average Distance Using % Identity</strong></li>
33 <li><strong>Neighbour Joining Using % Identity</strong></li>
34 <li><strong>Average Distance Using Blosum62</strong></li>
35 <li><strong>Neighbour Joining Using Blosum62<br>
39 <li><strong>Pairwise Alignments</strong><br>
40 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
41 alignments</a>.</em><br>
43 <li><strong>Principal Component Analysis</strong><br>
44 <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
45 in the alignment. See <a href="../calculations/pca.html">Principal Component
46 Analysis</a>.</em> <br>
48 <li><strong>Extract Scores ... (optional)</strong><br>
49 <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
50 When selected, these numbers are parsed into sequence associated annotation which can
51 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
54 <li><strong>Autocalculate Consensus</strong><br>
55 <em>For large alignments it can be useful to deselect "Autocalculate
56 Consensus" when editing. This prevents the sometimes lengthy calculations
57 performed after each sequence edit.</em> <br>