Alignment Window Menus
- 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 is a tab separated list:
NAME START_RES END_RES SEQUENCE
- 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
All gap characters ("-", ".") will be deleted from the alignment.
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
Adds gaps to the end of all the sequences so they are all the same length. This is useful for making a tree using unaligned sequences.
You may set the default gap character in preferences.
- Find
Select this to search for residues, sequence name or residue position within the alignment.
- Font
Change the font of the display from the "Choose Font" dialog box, which is shown when this item is selected.
- 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.
- 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.
- 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.
- 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.
- Sort
The Sort menu will have some additional options if you have just done a multiple alignment calculation, or opened a tree viewer window.
- 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.
- 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.
- 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.
- Clustal Alignment
Submits all, or just the currently selected sequences for alignment with clustal W.- Clustal 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 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.
- JNet
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).