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.
  - Select Highlighted Columns
    Selects the columns currently highlighted as a result of a find, mouse over, or selection event from a linked structure viewer or other application. Modifiers will work on some platforms: ALT will add all but the highlighted set to the column selection, and CTRL (or META) will toggle the selection.
- 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.
  - 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.
- 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, Purine/Pyrimidine, User Defined
    See colours for a description of all colour schemes.
  - Sequence ID
    Shades sequences using their Sequence ID colour. Useful when performing tree based subfamily analysis.
  - 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.
  - By RNA Helices
    Colours the helices of an RNA alignment loaded from a Stockholm file. See RNA Helices 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 or PCA ...
    Opens the calculations dialog for for calculating trees or principal component analysis plots on the alignment or the currently selected region.
  - Pairwise Alignments
    Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
  - 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.
  - Sort With New Tree
    When enabled, Jalview will automatically sort the alignment when a new tree is calculated or loaded onto it.
  - Show Flanking Regions
    Opens a new alignment window showing any additional sequence data either side of the current alignment. Useful in conjunction with 'Fetch Database References' when the 'Trim Retrieved Sequences' option is disabled to retrieve full length sequences for a set of aligned peptides.
- Web Service Menu
  This menu is dynamic, and may contain user-defined web service entries in addition to any of the following ones:
  - Fetch DB References
    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.
    - 'Trim Retrieved Sequences' - when checked, Jalview will discard any additional sequence data for accessions associated with sequences in the alignment.
      Note: Disabling this could cause out of memory errors when working with genomic sequence records !
      Added in Jalview 2.8.1
    - 'Standard Databases' will check sequences against the EBI databases.
    Other sub-menus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname.

  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 use these services through Jalview.

  - Alignment
    Align the currently selected sequences or all sequences in the alignment, or re-align unaligned sequences to the aligned sequences. Entries in this menu provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence Alignment webservice client entry for more information.
  - Secondary Structure Prediction
    - JPred Secondary Structure Prediction
      Secondary structure prediction by network consensus. See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:
      - If nothing is selected, and the displayed sequences appear to be aligned, then a JPred 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 JPred 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 JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
  - Analysis
    - Multi-Harmony
      Performs functional residue analysis on a protein family alignment with sub-families defined on it. See the Multi-Harmony service entry for more information.