Alignment Annotation
-In addition to the definition of groups, Jalview also allows you to mark particular - columns of an alignment and add symbols and text in the annotation area shown - below the alignment (which may be hidden if View→Show Annotation - is not ticked).
-As of Jalview 2.08 precalculated annotations can be added to alignments from - the command line, drag and drop, or from the "File-> Load Features / - Annotations" menu item. See the Annotations - File Format for more details.
- +In addition to the definition of groups and sequence features, + Jalview can display symbols and graphs under the columns of an + alignment, and allow you to mark particular columns of an alignment and add symbols and text + in the annotation area shown below the alignment (which may be hidden if View→Show + Annotation is not ticked).
+Web services can also add annotation to an alignment (see the + JNet web service), and as of Jalview 2.08 quantitative and symbolic + annotations can be added to an alignment via an Annotations + File dragged into the alignment window or loaded from the + alignment's file menu.
+Interactive Alignment Annotation
Annotation rows are added using the Annotation Label menu, which is obtained by clicking anywhere on the annotation row labels @@ -68,11 +70,8 @@ the row. Note: This cannot be undone
-Annotation is stored and retrieved using Jalview Archives. Quantitative -annnotation is also possible, but currently only possible with the -JNet web service, or by creating your own Jalview Archive (which -contains XML conforming to the Jalview-Vamsas XML schema). +User defined annotation is stored and retrieved using Jalview Archives.
Current Limitations
@@ -81,6 +80,8 @@ rows is not possible. If you save your annotation as a Jalview file, however, it will be reloaded with user annotations at the top (nearest the alignment), above any of the automatically generated Conservation, Quality or consensus -annotations. +annotations. Finally, the Jalview GUI will not, as yet, allow you to output +Jalview annotation files for the current alignment, change the line +colour, display style, or create groups of quantitative annotation rows.