3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Window Menus</title>
28 <strong>Alignment Window Calculate Menu</strong>
31 <li><strong>Sort </strong>
33 <li><strong>By ID</strong><em><br> This will sort
34 the sequences according to sequence name. If the sort is
35 repeated, the order of the sorted sequences will be
37 <li><strong>By Length</strong><em><br> This will
38 sort the sequences according to their length (excluding gap
39 characters). If the sort is repeated, the order of the
40 sorted sequences will be inverted. </em></li>
41 <li><strong>By Group</strong><strong><br> </strong><em>This
42 will sort the sequences according to sequence name. If the
43 sort is repeated, the order of the sorted sequences will be
44 inverted. </em><strong></strong></li>
45 <li><strong>By Pairwise Identity<br>
46 </strong><em>This will sort the selected sequences by their
47 percentage identity to the consensus sequence. The most
48 similar sequence is put at the top. </em></li>
49 <li><em>The <a href="../calculations/sorting.html">Sort
50 menu</a> will have some additional options if the alignment
51 has any associated score annotation, or you have just done a
52 multiple alignment calculation or opened a tree viewer
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
62 <li><strong>Neighbour Joining Using PAM250<br>
64 <li><strong>Neighbour Joining Using Sequence
65 Feature Similarity</strong></li>
66 <li><strong>Neighbour Joining Using Blosum62<br>
68 <li><strong>Neighbour Joining Using % Identity</strong></li>
69 <li><strong>Average Distance Using PAM250<br>
71 <li><strong>Average Distance Using Sequence
72 Feature Similarity</strong></li>
73 <li><strong>Average Distance Using Blosum62</strong></li>
74 <li><strong>Average Distance Using % Identity</strong></li>
76 <li><strong>Pairwise Alignments</strong><br> <em>Applies
77 Smith and Waterman algorithm to selected sequences. See <a
78 href="../calculations/pairwise.html"
79 >pairwise alignments</a>.
81 <li><strong>Principal Component Analysis</strong><br> <em>Shows
82 a spatial clustering of the sequences based on similarity scores
83 calculated over the alignment.. See <a
84 href="../calculations/pca.html"
85 >Principal Component Analysis</a>.
87 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
88 option is only visible if Jalview detects one or more
89 white-space separated values in the description line of the
90 alignment sequences.<br> When selected, these numbers are
91 parsed into sequence associated annotation which can then be
92 used to sort the alignment via the Sort by→Score menu.
94 <li><strong>Translate as cDNA</strong> (not applet)<br>
95 <em>This option is visible for nucleotide alignments. Selecting
96 this option shows the DNA's calculated protein product in a new
97 <a href="../features/splitView.html">split frame</a> window.
98 Note that the translation is not frame- or intron-aware; it
99 simply translates all codons in each sequence, using the
100 standard <a href="../misc/geneticCode.html">genetic code</a>
101 (any incomplete final codon is discarded). You can perform this
102 action on the whole alignment, or selected rows, columns, or
105 <li><strong>Reverse, Reverse Complement</strong> (not applet)<br>
106 <em>These options are visible for nucleotide alignments. Selecting them adds the reverse (or reverse complement)
107 of the sequences (or selected region) as new sequences in the alignment. To try this out, add this sequence and
108 perform 'Reverse Complement' followed by 'Translate as cDNA':
110 Seq GTCATTTGCGCGTGTTGATTATTCGGACCGCTCCACTTCCCTTTACTCGTGCGTTCAATTGATTTAATCCTC
111 TGGGGGGGCTCTGGTTTACATAGCTTAAATCTATTCCATTCAAGGAAGCTCATG</small>
113 <li><strong>Get Cross-References</strong> (not applet)<br>
114 <em>This option is visible where sequences have
115 cross-references to other standard databases; for example, an
116 EMBL entry may have cross-references to one or more UNIPROT
117 entries. Select the database to view all cross-referenced
118 sequences in a new <a href="../features/splitView.html">split
121 <li><strong>Autocalculate Consensus</strong><br> <em>For
122 large alignments it can be useful to deselect
123 "Autocalculate Consensus" when editing. This prevents
124 the sometimes lengthy calculations performed after each sequence
126 <li><strong>Sort Alignment With New Tree</strong><br> <em>If
127 this option is selected, the alignment will be automatically
128 sorted whenever a new tree is calculated or loaded.</em> <br></li>
129 <li><strong>Show Flanking Regions</strong><br> <em>Opens
130 a new alignment window showing any additional sequence data
131 either side of the current alignment. Useful in conjunction with
132 'Fetch Database References' when the 'Trim Retrieved Sequences'
133 option is disabled to retrieve full length sequences for a set
134 of aligned peptides. </em></li>