-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Calculate Menu</strong></p>\r
-<ul>\r
- <li><strong>Calculate</strong></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
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+ <p>
+ <strong>Alignment Window Calculate Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Sort </strong>
+ <ul>
+ <li><strong>by ID</strong><em><br> This will sort the
+ sequences according to sequence name. If the sort is repeated, the
+ order of the sorted sequences will be inverted. </em>
+ </li>
+ <li><strong>by Length</strong><em><br> This will sort
+ the sequences according to their length (excluding gap
+ characters). If the sort is repeated, the order of the sorted
+ sequences will be inverted. </em>
+ </li>
+ <li><strong>by Group</strong><strong><br> </strong><em>This
+ will sort the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
+ </li>
+ <li><strong>by Pairwise Identity<br> </strong><em>This
+ will sort the selected sequences by their percentage identity to
+ the consensus sequence. The most similar sequence is put at the
+ top. </em>
+ </li>
+ <li><em>The <a href="../calculations/sorting.html">Sort
+ menu</a> will have some additional options if the alignment has any
+ associated score annotation, or you have just done a multiple
+ alignment calculation or opened a tree viewer window.</em><br></li>
+ </ul></li>
+ <li><strong>Calculate Tree </strong> <br> <em>Functions
+ for calculating trees on the alignment or the currently selected
+ region. See <a href="../calculations/tree.html">calculating
+ trees</a>.</em>
+ <ul>
+ <li><strong>Average Distance Using % Identity</strong>
+ </li>
+ <li><strong>Neighbour Joining Using % Identity</strong>
+ </li>
+ <li><strong>Average Distance Using Blosum62</strong>
+ </li>
+ <li><strong>Neighbour Joining Using Blosum62<br>
+ </strong>
+ </li>
+ </ul></li>
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
+ </li>
+ <li><strong>Principal Component Analysis</strong><br> <em>Shows
+ a spatial clustering of the sequences based on the BLOSUM62 scores
+ in the alignment. See <a href="../calculations/pca.html">Principal
+ Component Analysis</a>.</em> <br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <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>
+ When selected, these numbers are parsed into sequence associated
+ annotation which can then be used to sort the alignment via the Sort
+ by→Score menu.</em> <br></li>
+
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
+ large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy
+ calculations performed after each sequence edit.</em> <br></li>
+ <li><strong>Sort Alignment With New Tree</strong><br> <em>If
+ this option is selected, the alignment will be automatically sorted
+ whenever a new tree is calculated or loaded.</em> <br>
+ </li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff