Alignment Window Menus
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-- Undo
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- 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
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- Any actions which you undo can be redone using redo.
-- Cut
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- 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
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- 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 -
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-- To New Alignment
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- 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
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- Copied sequences from another alignment window can be added - to the current Jalview alignment.
-- Delete
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- 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
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- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-- Deselect All
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- 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
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- Any sequence ids currently not selected will replace the current - selection.
-- Undefine Groups
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- The alignment will be reset with no defined groups.
WARNING: - This cannot be undone.
-- Remove Left
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- 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
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- 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
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- All columns which only contain gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences. -
-- Remove All Gaps
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- All gap characters ("-", ".") will be deleted from - the alignment.
- You may set the default gap character in preferences. -
-- Remove Redundancy
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- 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
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- 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. -
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-- Find
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- Select this to search - for residues, sequence name or residue position within the alignment.
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-- Font
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- Change the font of the display from the - "Choose Font" dialog box, which is shown when this - item is selected.
-- Wrap
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- 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
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- 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
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- 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
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- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
-- Colour Text
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- 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
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- 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
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- 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
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- 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
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- 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.
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-- Apply Colour To All Groups
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- 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
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- See colours for - a description of all colour schemes.
-- By Conservation
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- See Colouring - by Conservation.
-- Modify Conservation Threshold
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- 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
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- See Above Percentage - Identity.
-- Modify Identity Threshold
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- Use this to set the threshold value for colouring above Identity. - Useful if the window has been closed.
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- Sort -
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- 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
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- 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
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- 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
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- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
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-- Calculate Tree -
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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
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- Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
-- Principal Component Analysis
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- 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
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- Submits all, or just the currently selected sequences for alignment with clustal W.- Clustal Realign
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- 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.
-- JPred
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- 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). -
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