href="../features/featuresettings.html">Sequence
Feature Settings...</a> </strong><br> <em>Opens the
Sequence Feature Settings dialog box to control the colour
- and display of sequence features on the alignment, and
- configure and retrieve features from DAS annotation
- servers.</em></li>
+ and display of sequence features on the alignment.</em></li>
<li><strong>Sequence ID Tooltip</strong><em>
(application only) <br>This submenu's options allow the
inclusion or exclusion of non-positional sequence features
alignment (and within that, by label).</em></li>
<li><strong>Sort by Label</strong><em><br>Sort
sequence-specific annotations by label (and within that, by
- sequence order). If neither sort order is selected, no
- sorting is applied, allowing you to make a manual ordering
- of the annotations.</em></li>
+ sequence order).</em></li>
<li><strong>Autocalculated Annotation<br>
</strong><em>Settings for the display of autocalculated annotation.</em>
<ul>
</strong> <em>See <a href="../colourSchemes/index.html">colours</a>
for a description of all colour schemes.
</em><br></li>
- <li><strong>By Conservation<br>
+ <li><strong>Sequence ID<br></strong><em>Shades
+ sequences using their Sequence ID colour. Useful when
+ performing <a
+ href="../calculations/treeviewer.html#partitioning">tree
+ based subfamily analysis</a>.
+ </em></li>
+ <li><strong>By Conservation<br>
</strong><em>See <a href="../colourSchemes/conservation.html">Colouring
by Conservation</a>.
</em><br></li>
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
- <li><strong>Fetch DB References</strong><br> <em>This
- submenu contains options for accessing any of the database
- services that Jalview is aware of (e.g. DAS sequence servers
- and the WSDBFetch service provided by the EBI) to verify
- sequence start/end positions and retrieve all database cross
- references and PDB ids associated with all or just the
- selected sequences in the alignment.
- <ul>
- <li>'Trim Retrieved Sequences' - when checked, Jalview
- will discard any additional sequence data for accessions
- associated with sequences in the alignment. <br> <strong>Note:
- Disabling this could cause out of memory errors when
- working with genomic sequence records !</strong><br> <strong>Added
- in Jalview 2.8.1</strong>
- </li>
- <li>'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources</li>
- </ul> Other sub-menus allow you to pick a specific source to query
- - sources are listed alphabetically according to their
- nickname.
- </em><br></li>
- </ul>
+ <li><strong>Fetch DB References</strong><br> <em>This
+ submenu contains options for accessing any of the database
+ services that Jalview is aware of (e.g. those provided by
+ EMBL-EBI) to verify sequence start/end positions and retrieve all
+ database cross references and PDB ids associated with all or just
+ the selected sequences in the alignment.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ Disabling this could cause out of memory errors when working
+ with genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases.</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
+ </ul>
<p>Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee,
or elsewhere. You need a continuous network connection in order to