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 Length</strong><em><br>
13 This will sort the sequences according to their length (excluding gap characters). If the sort is
14 repeated, the order of the sorted sequences will be inverted. </em></li>
15 <li><strong>by Group</strong><strong><br>
16 </strong><em>This will sort the sequences according to sequence name.
17 If the sort is repeated, the order of the sorted sequences will be inverted.
18 </em><strong></strong></li>
19 <li><strong>by Pairwise Identity<br>
20 </strong><em>This will sort the selected sequences by their percentage
21 identity to the consensus sequence. The most similar sequence is put at
23 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
24 some additional options if the alignment has any associated
25 score annotation, or you have just done a multiple alignment calculation
26 or opened a tree viewer window.</em><br>
30 <li><strong>Calculate Tree </strong> <br>
31 <em>Functions for calculating trees on the alignment or the currently selected
33 href="../calculations/tree.html">calculating trees</a>.</em>
35 <li><strong>Average Distance Using % Identity</strong></li>
36 <li><strong>Neighbour Joining Using % Identity</strong></li>
37 <li><strong>Average Distance Using Blosum62</strong></li>
38 <li><strong>Neighbour Joining Using Blosum62<br>
42 <li><strong>Pairwise Alignments</strong><br>
43 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
44 alignments</a>.</em><br>
46 <li><strong>Principal Component Analysis</strong><br>
47 <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores
48 in the alignment. See <a href="../calculations/pca.html">Principal Component
49 Analysis</a>.</em> <br>
51 <li><strong>Extract Scores ... (optional)</strong><br>
52 <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>
53 When selected, these numbers are parsed into sequence associated annotation which can
54 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
57 <li><strong>Autocalculate Consensus</strong><br>
58 <em>For large alignments it can be useful to deselect "Autocalculate
59 Consensus" when editing. This prevents the sometimes lengthy calculations
60 performed after each sequence edit.</em> <br>