Alignment Window Menus

• File
  • Fetch Sequence
    Shows a dialog window in which you can retrieve known ids from Uniprot, EMBL, EMBLCDS, PFAM, Rfam, 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
    • PileUp
    • AMSA
    • STH
    • Phylip
    • JSON
  • Page Setup ...
    Open the printing system's Page Setup dialog box, to control page size, layout and orientation.
  • 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.
    • SVG
      Create a Scalable Vector Graphics file from your alignment for embedding in web pages.
    • BioJS
      Create a BioJS MSA Viewer HTML 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 from the Desktop's Save Project File menu option, 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 right of the rightmost 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 are no empty columns before or after the first or last aligned residue) and all sequences will be padded with gap characters 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.
  • Create Group (Control G)
    Create a group containing the currently selected sequences.
  • Remove Group (Shift Control G)
    Ungroup the currently selected sequence group.
  • Make Groups for selection
    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 at marked columns.
  • Undefine Groups (Control U)
    The alignment will be reset with no defined groups.
    WARNING: This cannot be undone.
  • Select/Hide Columns by Annotation
    Select or Hide columns in the alignment according to secondary structure, labels and values shown in alignment annotation rows.
• 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 Sequence Features
    Show or hide sequence features on this alignment.
  • Sequence 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.
• Annotations (Since Jalview 2.8.2)
  • 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.
  • Show Alignment Related
    Show all annotations that are for the alignment as a whole (for example, Consensus, or secondary structure prediction from alignment).
  • Hide Alignment Related
    Hide all annotations that are for the alignment as a whole.
  • Show Sequence Related
    Show all annotations that are for individual sequences.
  • Hide Sequence Related
    Hide all annotations that are for individual sequences.
  • You can also selectively show or hide annotations from the Popup or Annotation menus.
  • Sort by Sequence
    Sort sequence-specific annotations by sequence order in the alignment (and within that, by label).
  • Sort by Label
    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.
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation.
    • Show first
      Show autocalculated annotations above sequence-specific annotations. Note this also applies to other annotations for the alignment, for example secondary structure prediction from alignment.
    • Show last
      Show autocalculated / alignment annotations below sequence-specific annotations.
    • 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 Logo
      Enable or disable the display of the Consensus Logo above the consensus sequence.
    • Normalise Consensus Logo
      When enabled, scales all logo stacks to the same height, making it easier to compare symbol diversity in highly variable regions.
    • Group Conservation
      When ticked, display a conservation row for all groups (only available for protein alignments).
    • Group Consensus
      When ticked, display a consensus row for all groups.
• 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.