-<html>\r
-<head><title>Sequence Features</title></head>\r
-<body>\r
-<p><strong>Sequence Features</strong></p>\r
-<p>Jalview can colour parts of a sequence based on the presence of\r
-sequence features - which may be retrieved from database records (such\r
-as Uniprot), the result of <a href="search.html">sequence motif\r
-searches</a> or simply read from a <a\r
-href="featuresFormat.html">sequence features file</a>.</p>\r
-<p><strong>Sequence Feature Groups</strong></p>\r
-<p>Since Jalview 2.08, sequence features assigned to a sequence can be\r
-organised into groups, which may indicate that the features were all retrieved\r
-from the same database (such as Uniprot features), or generated by the\r
-same analysis process (as might be specified in a <a\r
-href="featuresFormat.html">sequence features file</a>).</p>\r
-<p><strong>Sequence Feature Inheritance</strong></p>\r
-<p>Since Jalview 2.08, sequence features are <em>global</em> to a set of\r
-sequences appearing (independently or together) in many different\r
-alignments. Practically, this means features loaded onto one alignment\r
-can be viewed in any alignments involving the same sequences. The same\r
-sequence appears in different alignments when a new alignment is\r
-generated by submitting an existing set of sequences to one of the\r
-alignment or prediction web services, and when sequences are copied\r
-and pasted into other alignment windows.</p>\r
-<p><strong>View→Show Sequence Features</strong></p>\r
-<p>Toggle the display of sequence features in this alignment. If\r
-feature retrieval has not already been carried out, then Jalview will\r
-automatically try to fetch sequence features (as described below).</p>\r
-<p><strong>View→Sequence Feature Settings...</strong>\r
-<p>Once sequence features have been loaded, their display can be fully controlled \r
- using the alignment window's <a\r
- href="featuresettings.html">Sequence Feature Settings</a> dialog box. Feature \r
- colour schemes and display parameters are unique to a particular alignment, \r
- so it is possible to colour the same sequence features differently in different \r
- alignment views.<br>\r
- Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS features</a> \r
- to an alignment via the DAS tabbed pane of the feature settings window. </p>\r
-<p>Precalculated Sequence Features may be added to an alignment from the command\r
- line, drag and drop, or from the "File->Load Features / Annotations"\r
- menu item. See the <a href="featuresFormat.html">Features File Format</a> for\r
- more details.</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Sequence Features</title>
+</head>
+<body>
+ <p>
+ <strong>Sequence Features</strong>
+ </p>
+ <p>
+ Jalview can colour parts of a sequence based on the presence of
+ sequence features - which may be retrieved from database records
+ (such as UniProt), the result of <a href="search.html">sequence
+ motif searches</a> or simply read from a <a href="featuresFormat.html">sequence
+ features file</a>. You can also <a href="creatinFeatures.html">create
+ features</a> from the results of searches or the current selection,
+ and <a href="editingFeatures.html">edit features</a> by double
+ clicking on them.
+ </p>
+ <p>
+ <strong>Sequence Feature Colouring Styles</strong>
+ </p>
+ <p>
+ By default, Jalview will assign a color to each feature based on its
+ type. These colours can be changed from the <a
+ href="featuresettings.html">feature settings</a> and <a
+ href="editingFeatures.html">amend features</a> dialog boxes. Since
+ Jalview 2.5, it is also possible to define <a
+ href="featureschemes.html">feature colourschemes</a> to shade
+ features based on their associated scores or text labels.
+ </p>
+ <p>
+ <strong>Sequence Feature Groups</strong>
+ </p>
+ <p>
+ Since Jalview 2.08, sequence features assigned to a sequence can be
+ organised into groups, which may indicate that the features were all
+ retrieved from the same database (such as UniProt features), or
+ generated by the same analysis process (as might be specified in a <a
+ href="featuresFormat.html">sequence features file</a>).
+ </p>
+ <p>
+ <strong>Sequence Feature Inheritance</strong>
+ </p>
+ <p>
+ Since Jalview 2.08, sequence features are <em>global</em> to a set
+ of sequences appearing (independently or together) in many different
+ alignments. Practically, this means features loaded onto one
+ alignment can be viewed in any alignments involving the same
+ sequences. The same sequence appears in different alignments when a
+ new alignment is generated by submitting an existing set of
+ sequences to one of the alignment or prediction web services, and
+ when sequences are copied and pasted into other alignment windows.
+ </p>
+ <p>
+ <strong>View→Show Sequence Features</strong>
+ </p>
+ <p>Toggle the display of sequence features in this alignment. If
+ feature retrieval has not already been carried out, then Jalview
+ will automatically try to fetch sequence features (as described
+ below).</p>
+ <p>
+ <strong>View→Sequence Feature Settings...</strong>
+ </p>
+ <p>
+ Once sequence features have been loaded, their display can be fully
+ controlled using the alignment window's <a
+ href="featuresettings.html">Sequence Feature Settings</a>
+ dialog box. Feature colour schemes and display parameters are unique
+ to a particular alignment, so it is possible to colour the same
+ sequence features differently in different alignment views.<br>
+ Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS
+ features</a> to an alignment via the DAS tabbed pane of the feature
+ settings window.
+ </p>
+ <p>
+ <strong>View→Sequence ID Tooltip→Show
+ Non-Positional features</strong><br> <em>Only available in
+ application</em></br>
+ </p>
+ <p>Toggles the display of non-positional features in the sequence
+ ID tooltip, and whether they will be included when sequence features
+ are exported using "File→Export Features".</p>
+ <p>
+ Precalculated Sequence Features may be added to an alignment from
+ the command line, drag and drop, or from the "File→Load
+ Features / Annotations" menu item. See the <a
+ href="featuresFormat.html">Features File Format</a> for more
+ details.
+ </p>
+</body>
+</html>