2 <head><title>Alignment Window Menus</title></head>
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5 <p><strong>Alignment Window Calculate Menu</strong></p>
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7 <li><strong>Calculate</strong></li>
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11 <li><strong>Sort </strong>
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13 <li><strong>by ID<br>
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14 </strong><em>This will sort the sequences according to sequence name.
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15 If the sort is repeated, the order of the sorted sequences will be inverted.
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18 <li><strong>by Group</strong><strong><br>
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19 </strong><em>This will sort the sequences according to sequence name.
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20 If the sort is repeated, the order of the sorted sequences will be inverted.
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21 </em><strong></strong><strong><br>
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23 <li><strong>by Pairwise Identity<br>
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24 </strong><em>This will sort the selected sequences by their percentage
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25 identity to the consensus sequence. The most similar sequence is put
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26 at the top. </em><strong><br>
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29 <em>The <a href="../calculations/sorting.html">Sort menu</a> will
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30 have some additional options if you have just done a multiple
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31 alignment calculation, or opened a tree viewer window.</em><br>
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33 <li><strong>Calculate Tree </strong>
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34 <br><em>Functions for calculating trees on the alignment or the
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35 currently selected region. See <a
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36 href="../calculations/tree.html">calculating trees</a>.</em>
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38 <li><strong>Average Distance Using % Identity</strong></li>
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39 <li><strong>Neighbour Joining Using % Identity</strong></li>
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40 <li><strong>Average Distance Using Blosum62</strong></li>
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41 <li><strong>Neighbour Joining Using Blosum62<br></strong></li>
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44 <li><strong>Pairwise Alignments</strong><br>
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45 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
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47 <li><strong>Principal Component Analysis</strong><br>
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48 <em>Shows a spatial clustering of the sequences based on the
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49 BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>
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52 <li><strong>Web Service<br>
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54 <em>Selecting one of the following menu items starts a remote service
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55 on compute facilities at the University of Dundee. You need a
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56 continuous network connection in order to use these services
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60 <li><strong>Clustal Alignment</strong><br><em>
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61 Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>
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62 <li><strong>Clustal Realign</strong><br><em>
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63 Submits the alignment or currently selected region for
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64 re-alignment with clustal W. Use this if you have added some
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65 new sequences to an existing alignment.</em><br></li>
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66 <li><strong>Muscle Alignment</strong><br><em>
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67 Submits all, or jut the currently selected sequences for
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68 alignment using Muscle. Do not use this if you are working with
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69 nucleic acid sequences.</em><br>
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70 <li><strong>JNet</strong><br><em>
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71 Secondary structure prediction by network consensus. The
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72 behaviour of this calculation depends on the current selection:
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74 <li>If nothing is selected, and the displayed sequences appear to
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75 be aligned, then a JNet prediction will be run for the first
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76 sequence in the alignment, using the current
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77 alignment. Otherwise the first sequence will be submitted for prediction.
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80 just one sequence (or a region on one sequence) has been selected,
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81 it will be submitted to the automatic JNet prediction server
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82 for homolog detection and prediction.
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84 <li>If a set of sequences are selected, and they appear to be aligned,
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85 then the alignment will be used for a Jnet prediction on the
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86 <strong>first</strong> sequence selected in the set (that is, the one
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87 that was first clicked on).
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