Alignment Window Menus

Alignment Window Menus

File

Fetch Sequence
Shows a dialog window in which you can select known ids from Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by the European Bioinformatics Institute. See Sequence Fetcher.
Add Sequences
Add sequences to the visible alignment from file, URL, or cut & paste window
Reload
Reloads the alignment from the original file, if available.
Warning: This will delete any edits, analyses and colourings applied since the alignment was last saved, and cannot be undone.
Save (Control S)
Saves the alignment to the file it was loaded from (if available), in the same format, updating the original in place.
Save As (Control Shift S)
Save the alignment to local file. A file selection window will open, use the "Files of type:" selection box to determine which alignment format to save as.
Output to Textbox
The alignment will be displayed in plain text in a new window, which you can "Copy and Paste" using the pull down menu, or your standard operating system copy and paste keys. The output window also has a "New Window" button to import the (possibly edited) text as a new alignment.
Select the format of the text by selecting one of the following menu items.
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
Print (Control P)
Jalview will print the alignment using the current fonts and colours of your alignment. If the alignment has annotations visible, these will be printed below the alignment. If the alignment is wrapped the number of residues per line of your alignment will depend on the paper width or your alignment window width, whichever is the smaller.
Export Image
Creates an alignment graphic with the current view's annotation, alignment background colours and group colours. If the alignment is wrapped, the output will also be wrapped and will have the same visible residue width as the open alignment.
- HTML
  Create a web page from your alignment.
- EPS
  Create an Encapsulated Postscript file from your alignment.
- PNG
  Create a Portable Network Graphics file from your alignment.
Export Features
All features visible on the alignment can be saved to file or displayed in a textbox in either Jalview or GFF format
Export Annotations
All annotations visible on the alignment can be saved to file or displayed in a textbox in Jalview annotations format.
Load Associated Tree
Jalview can view trees stored in the Newick file format, and associate them with the alignment. Note: the ids of the tree file and your alignment MUST be the same.
Load Features / Annotations
Load files describing precalculated sequence features or alignment annotations.
Close (Control W)
Close the alignment window. Make sure you have saved your alignment before you close - either as a Jalview project or by using the Save As menu.

Edit

Undo (Control Z)
This will undo any edits you make to the alignment. This applies to insertion or deletion of gaps, cutting residues or sequences from the alignment or pasting sequences to the current alignment or sorting the alignment. NOTE: It DOES NOT undo colour changes, adjustments to group sizes, or changes to the annotation panel.
Redo (Control Y)
Any actions which you undo can be redone using redo.
Cut (Control X)
This will make a copy of the currently selected residues before removing them from your alignment. Click on a sequence name if you wish to select a whole sequence.
Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
Copy (Control C)
Copies the currently selected residues to the system clipboard - you can also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX).
If you try to paste the clipboard contents to a text editor, you will see the format of the copied residues FASTA.
Paste
- To New Alignment (Control Shift V)
  A new alignment window will be created from sequences previously copied or cut to the system clipboard.
  Use <CTRL> and <SHIFT> and V(<APPLE> and <SHIFT;> and and V on MacOSX) to paste.
- Add To This Alignment (Control V)
  Copied sequences from another alignment window can be added to the current Jalview alignment.
Delete (Backspace)
This will delete the currently selected residues without copying them to the clipboard. Like the other edit operations, this can be undone with Undo.
Remove Left (Control L)
If the alignment has marked columns, the alignment will be trimmed to the left of the leftmost marked column. To mark a column, mouse click the scale bar above the alignment. Click again to unmark a column, or select "Deselect All" to deselect all columns.
Remove Right (Control R)
If the alignment has marked columns, the alignment will be trimmed to the left of the leftmost marked column. To mark a column, mouse click the scale bar above the alignment. Click again to unmark a column, or select "Deselect All" to deselect all columns.
Remove Empty Columns (Control E)
All columns which only contain gap characters ("-", ".") will be deleted.
You may set the default gap character in preferences.
Remove All Gaps (Control Shift E)
Gap characters ("-", ".") will be deleted from the selected area of the alignment. If no selection is made, ALL the gaps in the alignment will be removed.
You may set the default gap character in preferences.
Remove Redundancy (Control D)
Selecting this option brings up a window asking you to select a threshold. If the percentage identity between any two sequences (under the current alignment) exceeds this value then one of the sequences (the shorter) is discarded. Press the "Apply" button to remove redundant sequences. The "Undo" button will undo the last redundancy deletion.
Pad Gaps
When selected, the alignment will be kept at minimal width (so there no empty columns before or after the first or last aligned residue) and all sequences will be padded with gap characters to the before and after their terminating residues.
This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly aligned sequences' to be all the same length.
You may set the default for Pad Gaps in the preferences.

Select

Find... (Control F)
Opens the Find dialog box to search for residues, sequence name or residue position within the alignment and create new sequence features from the queries.
Select All (Control A)
Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
Deselect All (Escape)
Removes the current selection box (red dashed box) from the alignment window. All selected sequences, residues and marked columns will be deselected.
Use <ESCAPE> to deselect all.
Invert Sequence Selection (Control I)
Any sequence ids currently not selected will replace the current selection.
Invert Column Selection (Control Alt I)
Any columns currently not selected will replace the current column selection.
Undefine Groups (Control U)
The alignment will be reset with no defined groups.
WARNING: This cannot be undone.
Make Groups
The currently selected groups of the alignment will be subdivided according to the contents of the currently selected region.
Use this to subdivide an alignment based on the different combinations of residues observed at specific positions. (new in jalview 2.5)

View

New View (Control T)
Creates a new view from the current alignment view.
Expand Views (X)
Display each view associated with the alignment in its own alignment window, allowing several views to be displayed simultaneously.
Gather Views (G)
Each view associated with the alignment will be displayed within its own tab on the current alignment window.
Show→(all Columns / Sequences / Sequences and Columns)
All hidden Columns / Sequences / Sequences and Columns will be revealed.
Hide→(all Columns / Sequences / Selected Region / All but Selected Region )
Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.
Automatic Scrolling
When selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse pointer in a linked alignment or structure view.
Show Annotations
If this is selected the "Annotation Panel" will be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
Autocalculated Annotation
Settings for the display of autocalculated annotation.
- Apply to all groups
  When ticked, any modification to the current settings will be applied to all autocalculated annotation.
- Show Consensus Histogram
  Enable or disable the display of the histogram above the consensus sequence.
- Show Consensus Profile
  Enable or disable the display of the sequence logo above the consensus sequence.
- Group Conservation
  When ticked, display a conservation row for all groups (only available for protein alignments).
- Apply to all groups
  When ticked, display a consensus row for all groups.
Show Sequence Features
Show or hide sequence features on this alignment.
Seqence Feature Settings...
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.

Sequence ID Tooltip (application only)
This submenu's options allow the inclusion or exclusion of non-positional sequence features or database cross references from the tooltip shown when the mouse hovers over the sequence ID panel.

Alignment Properties...
Displays some simple statistics computed for the current alignment view and any named properties defined on the whole alignment.

Overview Window
A scaled version of the alignment will be displayed in a small window. A red box will indicate the currently visible area of the alignment. Move the visible region using the mouse.

Alignment Window Format Menu

Font...
Opens the "Choose Font" dialog box, in order to change the font of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster alignment rendering.

Wrap
When ticked, the alignment display is "wrapped" to the width of the alignment window. This is useful if your alignment has only a few sequences to view its full width at once.
Additional options for display of sequence numbering and scales are also visible in wrapped layout mode:

Scale Above
Show the alignment column position scale.

Scale Left
Show the sequence position for the first aligned residue in each row in the left column of the alignment.

Scale Right
Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.

Show Sequence Limits
If this box is selected the sequence name will have the start and end position of the sequence appended to the name, in the format NAME/START-END

Right Align Sequence ID
If this box is selected then the sequence names displayed in the sequence label area will be aligned against the left-hand edge of the alignment display, rather than the left-hand edge of the alignment window.

Show Hidden Markers
When this box is selected, positions in the alignment where rows and columns are hidden will be marked by blue arrows.

Boxes
If this is selected the background of a residue will be coloured using the selected background colour. Useful if used in conjunction with "Colour Text."

Text
If this is selected the residues will be displayed using the standard 1 character amino acid alphabet.

Colour Text
If this is selected the residues will be coloured according to the background colour associated with that residue. The colour is slightly darker than background so the amino acid symbol remains visible.

Show Gaps
When this is selected, gap characters will be displayed as "." or "-". If unselected, then gap characters will appear as blank spaces.
You may set the default gap character in preferences.

Centre Annotation Labels
Select this to center labels along an annotation row relative to their associated column (default is off, i.e. left-justified).

Show Unconserved
When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.

Colour

Apply Colour To All Groups
If this is selected, any changes made to the background colour will be applied to all currently defined groups.

Colour Text...
Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.

Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, User Defined
See colours for a description of all colour schemes.

By Conservation
See Colouring by Conservation.

Modify Conservation Threshold
Use this to display the conservation threshold slider window. Useful if the window has been closed, or if the 'by conservation' option appears to be doing nothing!

Above Identity Threshold
See Above Percentage Identity.

Modify Identity Threshold
Use this to set the threshold value for colouring above Identity. Useful if the window has been closed.

By Annotation
Colours the alignment on a per-column value from a specified annotation. See Annotation Colouring.

Calculate

Sort

by ID
This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.

by Length
This will sort the sequences according to their length (excluding gap characters). If the sort is repeated, the order of the sorted sequences will be inverted.

by Group
This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.

by Pairwise Identity
This will sort the selected sequences by their percentage identity to the consensus sequence. The most similar sequence is put at the top.

The Sort menu will have some additional options if you have just done a multiple alignment calculation, or opened a tree viewer window.

Calculate Tree
Functions for calculating trees on the alignment or the currently selected region. See calculating trees.

Average Distance Using % Identity

Neighbour Joining Using % Identity

Average Distance Using Blosum62

Neighbour Joining Using Blosum62

Pairwise Alignments
Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.

Principal Component Analysis
Shows a spatial clustering of the sequences based on the BLOSUM62 scores in the alignment. See Principal Component Analysis.

Extract Scores ... (optional)
This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
When selected, these numbers are parsed into sequence associated annotation which can then be used to sort the alignment via the Sort by→Score menu.

Autocalculate Consensus
For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after each sequence edit.

Web Service

Fetch DB References
This will use 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 the sequence and retrieve all database cross references and PDB ids associated with all or just the selected sequences in the alignment.

Selecting one of the following menu items starts a remote service on compute facilities at the University of Dundee. You need a continuous network connection in order to use these services through Jalview.

Alignment

ClustalW Multiple Sequence Alignment
Submits all, or just the currently selected sequences for alignment with clustal W.

ClustalW Multiple Sequence Alignment Realign
Submits the alignment or currently selected region for re-alignment with clustal W. Use this if you have added some new sequences to an existing alignment.

MAFFT Multiple Sequence Alignment
Submits all, or just the currently selected region for alignment with MAFFT.

Muscle Multiple Protein Sequence Alignment
Submits all, or just the currently selected sequences for alignment using Muscle. Do not use this if you are working with nucleic acid sequences.

Secondary Structure Prediction

JPred Secondary Structure Prediction
Secondary structure prediction by network consensus. The behaviour of this calculation depends on the current selection:

If nothing is selected, and the displayed sequences appear to be aligned, then a JNet prediction will be run for the first sequence in the alignment, using the current alignment. Otherwise the first sequence will be submitted for prediction.

If just one sequence (or a region on one sequence) has been selected, it will be submitted to the automatic JNet prediction server for homolog detection and prediction.

If a set of sequences are selected, and they appear to be aligned, then the alignment will be used for a Jnet prediction on the first sequence in the set (that is, the one that appears first in the alignment window).