- parameters</a>. <br> By default the item "EMBL-EBI Search" is added
- to this link menu. This link will show a web page in your default
- browser with the selected sequence id as part of the URL.<br>
- In the preferences dialog box, click <strong>new</strong> to add a
+ parameters</a>.</p>
+ <p>
+ By default, the list of available links in the preferences dialog box
+ contains the item "EMBL-EBI Search",
+ which is set as the URL which opens on double-clicking on a sequence ID, and as a
+ menu item in the Links menu. This link will show a web page in your default
+ browser with the selected sequence id as part of the URL.
+ <br>
+ Also by default, the list of available links contains persistent URLs for many common
+ bioinformatics databases. These links are downloaded by Jalview from
+ the <em>identifiers.org</em> website, and the names and URLs are not user editable.
+ <br>
+ The list of links is sortable, by clicking on the headers of the table. The list
+ can be filtered using the free text search box below the table, or the
+ "Custom Only" button, which displays only user-defined links.
+ </p>
+ <p>
+ In the preferences dialog box, the links which appear in the Links menu
+ can be configured by selecting or deselecting links in the "In Menu"
+ column. The names of selected links will be displayed
+ on new menu items under the "Link" menu when you right
+ click on a sequence id.<br>
+ You can configure which link is used when double-clicking on a sequence
+ by selecting or deselecting links in the "On Click" column. Exactly one
+ link must be configured for double-clicking. Since the link uses the sequence id
+ to construct the URL to open, the selected link must contain the
+ "$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$"
+ and other tokens).</p>
+ <p>
+ Additionally you can click <strong>new</strong> to add a