The preferences panel is opened from the Jalview Desktop’s Tools menu.
There are eight tabs in the Preferences dialog box:
Visual Preferences tab
Maximise Window - If this is selected, a new alignment window will stretch to fit the available space.
Open Overview Window - When this is selected, the alignment overview panel is opened by default for a new alignment window.
Show Annotations - If this is selected the new window will display an annotation panel below the sequences. This annotation panel may have several rows describing the whole alignment. The 4 standard annotations Conservation, Quality, Occupancy and Consensus for the alignment may be shown or hidden by default using the checkboxes adjacent and below.
Show group: Conservation and Consensus controls the display of per-group automatic annotation.
Consensus: Histogram and Logo checkboxes control the display of the consensus histogram and sequence logo for consensus annotation rows.
Full Sequence ID - If selected the ID panel will display the name of a sequence plus the start and end residues in the format name/start-end. If not selected, the displayed ID will be the name of the sequence.
Right Align IDs - select to align all sequence IDs to the left-hand edge of the sequence alignment, rather than the left-hand edge of the alignment display window.
Font - The default font name, size and style can be set for a new alignment window.
Sequence ID Tooltip: Control the display of Database References and Non-positional annotation in the tooltip displayed when the mouse is over a sequence's ID.
Show Unconserved - When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
Sequence Name Italics - select to apply the italicised version of the font to sequence labels.
Smooth Font - Toggles anti-aliasing on / off for faster rendering of the alignment.
Gap Symbol - The default gap symbol may be set to either "-" or "."
Wrap Alignment - Select whether to open new alignment windows in wrapped mode or not.
Sort alignment by - When the alignment is loaded in, it can be ordered as read (No sort), or sorted by Id or pairwise identity.
Sort annotations by - Annotations can be unsorted, sorted by the order of the related sequences in the alignment, or by label. Autocalculated annotations (e.g. Consensus) can be shown either last (below sequence annotations) or first (above sequence annotations). Since Jalview 2.8.2.
Open file - If this is selected then the default alignment
file will be opened when Jalview is started. You can change the
default file by clicking on file name and either typing in the file
path or selecting it from the file chooser window.
Note: The default example alignment is updated periodically to demonstrate new features in Jalview.
"Colours" Preferences tab
Alignment Colour - The default colour scheme for a new alignment window. If the chosen option is "User Defined" then the last User Defined Colour loaded or saved via the User Defined Colours panel will be loaded.
Annotation Shading Default - set the default minimum and maximum colours used when Colour by Annotation... is selected from the alignment window's colours menu.
"Overview" Preferences tab
Use legacy gap colouring (gaps are white) - when enabled, Jalview's overview shows gaps as white, and sequences with no colourscheme applied as grey.
Show Hidden regions when opening overview - default setting for inclusion of hidden regions.
Gap Colour - When legacy gap colouring is not enabled, this configures the default colour for gaps in the overview.
Hidden Colour - colour used to highlight regions in the overview that are hidden in the alignment.
"Structure" Preferences tab added in Jalview 2.8.2
Process secondary structure from PDB - if selected, then structure information read from PDB will be processed and annotation added to associated sequences.
Use RNAView for secondary structure - if selected, the pyRNA RNAView service (https://github.com/fjossinet/PyRNA) will be called to derive secondary structure information for RNA chains.
Add secondary structure annotation to alignment - if selected, Jmol's implementation DSSP will be used to add annotation to polypeptide chains in the structure.
Add Temperature Factor annotation to alignment - if selected, values extracted from the Temperature Factor column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
Default structure viewer - choose Jmol or CHIMERA for viewing 3D structures.
Path to Chimera program - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS. If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program. Double-click this field to open a file chooser dialog.
PDB Fields shown in Search and Structure Summaries - ticks in this table indicate fields shown by default when browsing results of a free text search via the PDB sequence fetcher, or 3D structures offered by the 3D Structure Chooser.
"Connections" Preferences tab
Default Browser (Unix)
It's difficult in Java to detect the default web browser for Unix users. If Jalview can't find your default web browser, enter the name or full path to your web browser application.
If you normally use a proxy server for using the internet, you must tick the box "Use a Proxy Server" and enter the address and port details as necessary. Web Services will not work if you are using a proxy server and do not enter the settings here.
Usage statistics, Questionnaire and Version checks
Uncheck these options to prevent Jalview from submitting usage statistics to google analytics, checking for Jalview questionnaires or retrieving details of the latest release version (at www.jalview.org). See the user privacy statement for more information.
The "Backups" Preferences Tab
Since Jalview 2.11.0, overwriting an existing file when saving or exporting data will by default trigger a backup file to be created. Several options are provided to control how backup files are named, and how many old versions will be kept.
Schemes - select from three default schemes Single Backup, Keep All Versions, and Rolled Backup Files, or choose Custom to enable a previously defined custom scheme.
Custom - Check this box to adjust the parameters of the currently selected scheme. Once OK is selected these parameters will be saved as the Custom scheme in your user preferences. To revert changes hit Cancel.
Scheme Examples - shows how backup files will appear according to the currently selected scheme and parameters.
Deleting Old Backup Files - these settings control how many backups are kept.
Backup filename strategy - specify the naming convention for numbered backups and how they are ordered.
The "Links" Preferences tab
This panel shows a table, and two sections - Edit and Filter. The table shows the available URL link definitions (consisting of a database, Name, and URL template string), a checkbox In Menu which indicates if the link is enabled, and Double Click which marks the link that will be opened if a sequence's ID is double clicked. The table can be sorted by clicking on the column headers.
This section contains three buttons, New, Edit and Delete, which allow you to create, modify and remove user-defined URL links from the Sequence ID's links submenu.
The Filter text box allows you to quickly show rows in the table containing a particular text string. The Custom only button limits the entries in the table to just those you have configured yourself via the Edit Links buttons. Press Show all to clear any filters.
The links table is prepopulated with persistent URLs for many common bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from the identifiers.org website, and the names and URLs are not user editable. Read more about configuring URL links.
Output Preferences tab
EPS Rendering Style
This is a selection box which allows the user to set a default rendering style for EPS export:
Automatically set ID width
When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.
Figure ID column width
Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if "Automatically set ID width" is set.
The output tab also has a group of checkboxes for each file format. If these are ticked, then Jalview will write files with the start and end sequence positions appended to each sequence id:
If the boxes are left unchecked for a particular format, the sequence limits will not be appended to the sequence id.
Embed BioJSON to HTML export
When this option is enabled, Jalview embeds BioJSON data within HTML files exported from Jalview at generation time. This enables the exported HTML files to be extracted and imported back into the Jalview desktop application at a later time.
Use Modeller Output
This option only applies to PIR format output. Jalview automatically reads PIR files with sequence descriptions compatible with the program Modeller. If this option is selected Jalview will write Modeller style PIR files with correct start/end numbering and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected.
"Editing" Preferences tab
There are currently three options available which can be selected / deselected.
AutoCalculate Consensus - For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents lengthy calculations which are performed after each sequence edit. New alignment windows will have their "Autocalculate Consensus" option set according to this setting.
Pad Gaps when Editing - New alignment windows will "Pad Gaps" according to this setting.
Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.
Web Services Preferences - documentation for this tab is given in the Web Services Preferences section.