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.
  • Save As
    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.
  • Export
    Creates an alignment graphic with the current 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.
  • 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.
    Select the format of the text by selecting one of the following menu items.
    • FASTA
    • MSF
    • CLUSTAL
    • BLC
    • PIR
    • PFAM
  • Print
    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.
  • 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
    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
    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
    Any actions which you undo can be redone using redo.
  • Cut
    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
    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
      A new alignment window will be created from sequences previously copied or cut to the system clipboard.
      Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
    • Add To This Alignment
      Copied sequences from another alignment window can be added to the current Jalview alignment.
  • Delete
    This will delete the currently selected residues without copying them to the clipboard. Like the other edit operations, this can be undone with Undo.
  • Select All
    Selects all the sequences and residues in the alignment.
    Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
  • Deselect All
    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 Selection
    Any sequence ids currently not selected will replace the current selection.
  • Undefine Groups
    The alignment will be reset with no defined groups.
    WARNING: This cannot be undone.
  • Remove Left
    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
    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
    All columns which only contain gap characters ("-", ".") will be deleted.
    You may set the default gap character in preferences.
  • Remove All Gaps
    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
    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.
  
  
• Search
  • Find
    Select this to search for residues, sequence name or residue position within the alignment and create new sequence features from the queries.
    
• View
  • Font
    Change the font of the display from the "Choose Font" dialog box, which is shown when this item is selected.
  • Smooth Fonts
    If selected, the alignment will be drawn with anti-aliasing on which looks better, but performace is reduced.
  • 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.
    Options are available to show the residue numbering at the start and/or end of an alignment as well as showing the alignment position above each sequence row.
    NOTE: When in wrapped alignment view, the alignment cannot be edited or have regions selected on it.
  • Show Full Sequence ID
    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
  • 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.
  • 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.
  • Fetch Sequence Features
    If the sequence names are Swissprot entries Jalview will use the names to retrieve sequence features from the EBI. Features which are 1 residue in length are coloured red, sequences longer than 1 residue are coloured blue. Move the mouse over a coloured feature to display the details of the feature.
    Note: The retrieved information will update the sequence start and end labels if they are incorrect.
  • Show Sequence Features
    Show or hide sequence features on this alignment.
  • Seqence Feature Settings...
    Control the colour and display of sequence features on the alignment. See Sequence Feature Settings.
    
  • 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.
• 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 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 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.
  • Translate cDNA
    If you are viewing a cDNA alignment a very simple translation service is available. The translation ignores all gaps in the cDNA sequences.
    
• Web Service
  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.
    • Muscle Multiple Protein Sequence Alignment
      Submits all, or jut 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 selected in the set (that is, the one that was first clicked on).