\r
<body>\r
<p><strong>Alignment Window Calculate Menu</strong></p>\r
+<strong>Calculate</strong> \r
<ul>\r
- <li><strong>Calculate</strong></li>\r
+ <li><strong>Sort </strong> \r
+ <ul>\r
+ <li><strong>by ID</strong><em><br>\r
+ This will sort the sequences according to sequence name. If the sort is \r
+ repeated, the order of the sorted sequences will be inverted. </em></li>\r
+ <li><strong>by Group</strong><strong><br>\r
+ </strong><em>This will sort the sequences according to sequence name. \r
+ If the sort is repeated, the order of the sorted sequences will be inverted. \r
+ </em><strong></strong></li>\r
+ <li><strong>by Pairwise Identity<br>\r
+ </strong><em>This will sort the selected sequences by their percentage \r
+ identity to the consensus sequence. The most similar sequence is put at \r
+ the top. </em></li>\r
+ <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have \r
+ some additional options if you have just done a multiple alignment calculation, \r
+ or opened a tree viewer window.</em><br>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Calculate Tree </strong> <br>\r
+ <em>Functions for calculating trees on the alignment or the currently selected \r
+ region. See <a\r
+ href="../calculations/tree.html">calculating trees</a>.</em> \r
+ <ul>\r
+ <li><strong>Average Distance Using % Identity</strong></li>\r
+ <li><strong>Neighbour Joining Using % Identity</strong></li>\r
+ <li><strong>Average Distance Using Blosum62</strong></li>\r
+ <li><strong>Neighbour Joining Using Blosum62<br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Pairwise Alignments</strong><br>\r
+ <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise \r
+ alignments</a>.</em><br>\r
+ </li>\r
+ <li><strong>Principal Component Analysis</strong><br>\r
+ <em>Shows a spatial clustering of the sequences based on the BLOSUM62 scores \r
+ in the alignment. See <a href="../calculations/pca.html">Principal Component \r
+ Analysis</a>.</em> <br>\r
+ </li>\r
+ <li><strong>Autocalculate Consensus</strong><br>\r
+ <em>For large alignments it can be useful to deselect "Autocalculate \r
+ Consensus" when editing. This prevents lengthy calculations which are \r
+ performed after each sequence edit.</em> <br>\r
+ </li>\r
</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Sort </strong>\r
- <ul>\r
- <li><strong>by ID<br>\r
- </strong><em>This will sort the sequences according to sequence name.\r
- If the sort is repeated, the order of the sorted sequences will be inverted.\r
- </em><strong><br>\r
- </strong></li>\r
- <li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name.\r
- If the sort is repeated, the order of the sorted sequences will be inverted.\r
- </em><strong></strong><strong><br>\r
- </strong></li>\r
- <li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage\r
- identity to the consensus sequence. The most similar sequence is put\r
- at the top. </em><strong><br>\r
- </strong></li>\r
- </ul>\r
- <em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
- have some additional options if you have just done a multiple\r
- alignment calculation, or opened a tree viewer window.</em><br>\r
- </li>\r
- <li><strong>Calculate Tree </strong>\r
- <br><em>Functions for calculating trees on the alignment or the\r
- currently selected region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em>\r
- <ul>\r
- <li><strong>Average Distance Using % Identity</strong></li>\r
- <li><strong>Neighbour Joining Using % Identity</strong></li>\r
- <li><strong>Average Distance Using Blosum62</strong></li>\r
- <li><strong>Neighbour Joining Using Blosum62<br></strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
- </li>\r
- <li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the\r
- BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
- <br>\r
- </li>\r
- <li><strong>Web Service<br>\r
- </strong>\r
- <em>Selecting one of the following menu items starts a remote service\r
- on compute facilities at the University of Dundee. You need a\r
- continuous network connection in order to use these services\r
- through Jalview.\r
- </em>\r
- <ul>\r
- <li><strong>Clustal Alignment</strong><br><em>\r
- Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>\r
- <li><strong>Clustal Realign</strong><br><em>\r
- Submits the alignment or currently selected region for\r
- re-alignment with clustal W. Use this if you have added some\r
- new sequences to an existing alignment.</em><br></li>\r
- <li><strong>Muscle Alignment</strong><br><em>\r
- Submits all, or jut the currently selected sequences for\r
- alignment using Muscle. Do not use this if you are working with\r
- nucleic acid sequences.</em><br>\r
- <li><strong>JNet</strong><br><em>\r
- Secondary structure prediction by network consensus. The\r
- behaviour of this calculation depends on the current selection:\r
- <ul>\r
- <li>If nothing is selected, and the displayed sequences appear to\r
- be aligned, then a JNet prediction will be run for the first\r
- sequence in the alignment, using the current\r
- alignment. Otherwise the first sequence will be submitted for prediction.\r
- </li>\r
- <li>If\r
- just one sequence (or a region on one sequence) has been selected,\r
- it will be submitted to the automatic JNet prediction server\r
- for homolog detection and prediction.\r
- </li>\r
- <li>If a set of sequences are selected, and they appear to be aligned,\r
- then the alignment will be used for a Jnet prediction on the\r
- <strong>first</strong> sequence selected in the set (that is, the one\r
- that was first clicked on).\r
- </li>\r
- </ul>\r
- </li>\r
- <p> </p>\r
-</ul>\r
-</blockquote>\r
-\r
-</body>\r
+ </body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff