Alignment Menu
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-- 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
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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
-
- 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
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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
-
- 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 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 reomove 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. -
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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. 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
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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 to enable the residue to be read.
-- Show Gaps
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- 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
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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 - calulation, 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.
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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.
-- 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
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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.- Above Identity Threshold
-
- 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.
-- - + + + +-
-- Sort -
--
-- 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.
-- Calculate Tree -
--
-- Average Distance Using % Identity
-- Neighbour Joining Using % Identity
-- Average Distance Using Blosum62
-- Neighbour Joining Using Blosum62
-
- See calculating trees. -
-- Paiwise Alignments
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- See pairwise alignments.
-- Principal Component Analysis
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- See Principal Component Analysis. -
-- Web Service
-
- -- Selecting one of the following menu items will start a remote service - on the high powered computing faciltiy 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
--
+ Alignment Window Menus +
+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. +
+