Alignment Menu
- 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. It DOES NOT undo colour changes or adjustments to group sizes affect 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. The format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE
Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.
- 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 making a copy of them first.
- 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 contain purely 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 two sequences exceeds this value one of the sequences (the shorter) is discarded. Press the "Apply" button to remove redundant sequences.
- Pad Gaps
If the sequences in an alignment window are not all the same length they can all be set to the length of the longest sequence by selecting "Pad Gaps." Any sequences which are shorter than the longest sequence in an alignment will have gap characters ("-" or ".") appended to the beginning or end to make them equal length.
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. The default font can be set from the "Choose Font" window, which is shown when the "Font Menu" is selected.
- Wrap
The default alignment display shows sequences in a single horizontal row. If your alignment has only a few sequences you may wish to "Wrap" the alignment so that the sequences are shown on multiple horizontal rows. 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: In the current version the wrap alignment should be used for viewing, not editing.
- 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 to enable the residue to be read.
- Show Gaps
If this is selected gap characters will be displayed as "." or "-". If unselected 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.
- 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.- 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
- 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
- Average Distance Using % Identity
- Neighbour Joining Using % Identity
- Average Distance Using Blosum62
- Neighbour Joining Using Blosum62
See calculating trees.
- Pairwise Alignments
See pairwise alignments.
- Principal Component Analysis
See Principal Component Analysis.
- Web Service
Selecting one of the following menu items will start a remote service on the high powered computing facility at the University of Dundee. You will need a continuous network connection in order to use these services.
- Clustal Alignment
- Clustal Realign
- JPred
- Muscle Alignment