<body>\r
<p><strong>Alignment Annotation</strong></p>\r
\r
-<p>In addition to the definition of groups and sequence features, Jalview also \r
- allows you to mark particular columns of an alignment and add symbols and text \r
+<p>In addition to the definition of groups and sequence features,\r
+ Jalview can display symbols and graphs under the columns of an\r
+ alignment, and allow you to mark particular columns of an alignment and add symbols and text \r
in the annotation area shown below the alignment (which may be hidden if <strong>View→Show \r
Annotation</strong> is not ticked). </p>\r
-<p>As of Jalview 2.08 precalculated annotations can be added to alignments from \r
- the command line, drag and drop, or from the "File-> Load Features / \r
- Annotations" menu item. See the <a href="annotationsFormat.html">Annotations \r
- File Format</a> for more details.</p>\r
+<p>Web services can also add annotation to an alignment (see the\r
+ <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic\r
+ annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations \r
+ File</a> for more details.</p>\r
\r
<p>\r
Annotation rows are added using the <strong>Annotation Label</strong>\r
</li>\r
</ul>\r
<p>\r
-Annotation is stored and retrieved using <a\r
-href="../features/jalarchive.html">Jalview Archives</a>. Quantitative\r
-annnotation is also possible, but currently only possible with the\r
-JNet web service, or by creating your own Jalview Archive (which\r
-contains XML conforming to the Jalview-Vamsas XML schema).\r
+User defined annotation is stored and retrieved using <a\r
+href="../features/jalarchive.html">Jalview Archives</a>.\r
</p>\r
<p><em>Current Limitations</em></p>\r
\r
git://source.jalview.org / jalview.git / blobdiff