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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Alignment Window Menus
-Alignment Window Menus
- File
+
+ Alignment Window Menus
+
- - 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.
- - Add Sequences
- Add sequences to the visible alignment from file, URL, or cut &
- paste window
- - Reload
- Reloads the alignment from the original file, if available.
- Warning: This will delete any edits, analyses and
- colourings applied since the alignment was last saved, and cannot be
- undone.
- - Save (Control S)
- Saves the alignment to the file it was loaded from (if available), in
- the same format, updating the original in place.
- - Save As (Control Shift S)
- 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.
- - 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. The
- output window also has a "New Window"
- button to import the (possibly edited) text as a new alignment.
- Select the format of the text by selecting one of the following menu
- items.
-
- - FASTA
- - MSF
- - CLUSTAL
- - BLC
- - PIR
- - PFAM
-
-
- - Print (Control P)
- 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.
-
- - Export Image
- Creates an alignment graphic with the current view's 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.
-
-
- - Export Features
- All features visible on the alignment can be saved to file or
- displayed in a textbox in either Jalview or GFF format
- - Export Annotations
- All annotations visible on the alignment can be saved to file or
- displayed in a textbox in Jalview annotations format.
- - 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 (Control W)
- 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.
-
+ File
+
+ - Fetch Sequence
Shows a
+ dialog window in which you can retrieve known ids from Uniprot,
+ EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
+ European Bioinformatics Institute. See Sequence Fetcher .
+ - Add Sequences
Add
+ sequences to the visible alignment from file, URL, or cut &
+ paste window
+
+ - Reload
Reloads the
+ alignment from the original file, if available.
Warning:
+ This will delete any edits, analyses and colourings applied since
+ the alignment was last saved, and cannot be undone.
+
+ - Save (Control S)
Saves
+ the alignment to the file it was loaded from (if available), in
+ the same format, updating the original in place.
+
+ - Save As (Control Shift S)
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.
+
+ - 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. The output
+ window also has a "New Window" button
+ to import the (possibly edited) text as a new alignment.
+ Select the format of the text by selecting one of the following
+ menu items.
+
+ - FASTA
+
+ - MSF
+
+ - CLUSTAL
+
+ - BLC
+
+ - PIR
+
+ - PFAM
+
+
+ - Print (Control P)
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.
+
+ - Export Image
Creates an
+ alignment graphic with the current view's 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.
+
+ - Export Features
All
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format
+
+ - Export Annotations
All
+ annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format.
+
+ - 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 (Control W)
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 (Control Z)
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 (Control Y)
Any
+ actions which you undo can be redone using redo.
+
+ - Cut (Control X)
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 (Control C)
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 (Control Shift V)
+ A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard.
Use
+ <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.
+
+ - Add To This Alignment (Control V)
+ Copied sequences from another alignment window can be
+ added to the current Jalview alignment.
+
+
+ - Delete (Backspace)
This
+ will delete the currently selected residues without copying them
+ to the clipboard. Like the other edit operations, this can be
+ undone with Undo.
+
+ - Remove Left (Control L)
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 (Control R)
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 (Control E)
+ All columns which only contain gap characters
+ ("-", ".") will be deleted.
You may
+ set the default gap character in preferences.
+
+ - Remove All Gaps (Control Shift E)
+ 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 (Control D)
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.
+
+
+ Select
+
+ - Find...
+ (Control F)
Opens the Find dialog box to
+ search for residues, sequence name or residue position within the
+ alignment and create new sequence features from the queries.
+
+ - Select All (Control A)
Selects
+ all the sequences and residues in the alignment.
Use
+ <CTRL> and A (<APPLE> and A on a MacOSX) to select
+ all.
+ - Deselect All (Escape)
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 Sequence Selection (Control I)
+ Any sequence ids currently not selected will replace the
+ current selection.
+
+ - Invert Column Selection (Control Alt I)
+ Any columns currently not selected will replace the current
+ column selection.
+
+ - Create Group (Control G)
+ Create a group containing the currently selected sequences.
+ - Remove Group (Shift Control G)
+ Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)
+ - Make Groups for selection
The currently
+ selected groups of the alignment will be subdivided according to
+ the contents of the currently selected region.
Use this to
+ subdivide an alignment based on the different combinations of
+ residues observed at specific positions. (new in jalview 2.5)
+
+ - Undefine Groups (Control U)
The
+ alignment will be reset with no defined groups.
WARNING:
+ This cannot be undone.
+
+
+ View
+
+ - New View (Control T)
+ Creates a new view from the current alignment view.
+
+ - Expand Views (X)
Display
+ each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously.
+
+ - Gather Views (G)
Each
+ view associated with the alignment will be displayed within its
+ own tab on the current alignment window.
+
+ - Show→(all Columns / Sequences /
+ Sequences and Columns)
All hidden Columns /
+ Sequences / Sequences and Columns will be revealed.
+
+ - Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region )
+ Hides the all the currently selected Columns / Sequences / Region
+ or everything but the selected Region.
+
+ - Automatic Scrolling
When
+ selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under
+ the mouse pointer in a linked alignment or structure view.
+ - 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.
+
+ - Autocalculated Annotation
Settings
+ for the display of autocalculated annotation.
+
+ - Apply to all groups
When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.
+ - Show Consensus Histogram
+ Enable or disable the display of the histogram above the
+ consensus sequence.
+ - Show Consensus Logo
Enable
+ or disable the display of the Consensus Logo above the consensus
+ sequence.
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+ - Group Conservation
When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).
+ - Apply to all groups
When
+ ticked, display a consensus row for all groups.
+
+ - Show Sequence Features
Show
+ or hide sequence features on this alignment.
+
+ - Seqence
+ Feature Settings...
Opens the
+ Sequence Feature Settings dialog box to control the colour and
+ display of sequence features on the alignment, and configure and
+ retrieve features from DAS annotation servers.
+
+ - Sequence ID Tooltip (application
+ only)
This submenu's options allow the inclusion or
+ exclusion of non-positional sequence features or database cross
+ references from the tooltip shown when the mouse hovers over the
+ sequence ID panel.
+
+ - Alignment Properties...
Displays
+ some simple statistics computed for the current alignment view and
+ any named properties defined on the whole alignment.
+
+ - 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.
+
+
+ Alignment Window Format Menu
+
+ - Font...
Opens the
+ "Choose Font" dialog box, in order to change the font of
+ the display and enable or disable 'smooth fonts' (anti-aliasing)
+ for faster alignment rendering.
+ - 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.
+ Additional options for display of sequence numbering and scales are
+ also visible in wrapped layout mode:
+
+ - Scale Above
Show the alignment
+ column position scale.
+ - Scale Left
Show the sequence
+ position for the first aligned residue in each row in the left
+ column of the alignment.
+ - Scale Right
Show the sequence
+ position for the last aligned residue in each row in the
+ right-most column of the alignment.
+ - Show Sequence Limits
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
+
+ - Right Align Sequence ID
If
+ this box is selected then the sequence names displayed in the
+ sequence label area will be aligned against the left-hand edge
+ of the alignment display, rather than the left-hand edge of the
+ alignment window.
+
+ - Show Hidden Markers
When
+ this box is selected, positions in the alignment where rows and
+ columns are hidden will be marked by blue arrows.
+
+ - 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.
+
+ - Centre Annotation Labels
Select
+ this to center labels along an annotation row relative to their
+ associated column (default is off, i.e. left-justified).
+
+ - Show Unconserved
When
+ this is selected, all consensus sequence symbols will be
+ rendered as a '.', highlighting mutations in highly conserved
+ alignments.
+
+
+
+
- Edit
-
- - Undo (Control Z)
- 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 (Control Y)
- Any actions which you undo can be redone using redo.
- - Cut (Control X)
- 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 (Control C)
- 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 (Control Shift V)
- A new alignment window will be created from sequences
- previously copied or cut to the system clipboard.
- Use <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> and and V on MacOSX) to paste.
- - Add To This Alignment (Control V)
- Copied sequences from another alignment window can be added
- to the current Jalview alignment.
+
- - Delete (Backspace)
- This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations, this
- can be undone with Undo.
- - Remove Left (Control L)
- 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 (Control R)
- 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 (Control E)
- All columns which only contain gap characters ("-",
- ".") will be deleted.
- You may set the default gap character in preferences.
- - Remove All Gaps (Control Shift E)
- 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 (Control D)
- 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.
-
-
- Select
-
- - Find...
- (Control F)
- Opens the Find dialog box to search for residues, sequence name or
- residue position within the alignment and create new sequence features
- from the queries.
- - Select All (Control A)
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
- all.
- - Deselect All (Escape)
- 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 Sequence Selection (Control I)
- Any sequence ids currently not selected will replace the
- current selection.
- - Invert Column Selection (Control Alt I)
- Any columns currently not selected will replace the current
- column selection.
- - Undefine Groups (Control U)
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.
- - Make Groups
- The currently selected groups of the alignment will be
- subdivided according to the contents of the currently selected region.
-
Use this to subdivide an alignment based on the
- different combinations of residues observed at specific
- positions. (new in jalview 2.5)
-
-
- View
-
- - New View (Control T)
- Creates a new view from the current alignment view.
- - Expand Views (X)
- Display each view associated with the alignment in its own alignment
- window, allowing several views to be displayed simultaneously.
- - Gather Views (G)
- Each view associated with the alignment will be displayed within its
- own tab on the current alignment window.
- - Show→(all Columns / Sequences / Sequences and Columns)
- All hidden Columns / Sequences / Sequences and Columns will be revealed.
- - Hide→(all Columns / Sequences / Selected Region / All but Selected Region )
- Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.
- - Automatic Scrolling
- When selected, the view will automatically scroll to display the
- highlighted sequence position corresponding to the position under the mouse
- pointer in a linked alignment or structure view.
-
- - 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.
- - Autocalculated Annotation
Settings for the display of autocalculated annotation.
- -
- Apply to all groups
- When ticked, any modification to the current settings will be applied to all autocalculated annotation.
-
- -
- Show Consensus Histogram
- Enable or disable the display of the histogram above the consensus sequence.
-
- -
- Show Consensus Profile
- Enable or disable the display of the sequence logo above the consensus sequence.
-
- -
- Group Conservation
- When ticked, display a conservation row for all groups (only available for protein alignments).
-
- -
- Apply to all groups
- When ticked, display a consensus row for all groups.
-
-
-
- - Show Sequence Features
- Show or hide sequence features on this alignment.
- - Seqence
- Feature Settings...
- Opens the Sequence Feature Settings dialog box to control the
- colour and display of sequence features on the alignment, and
- configure and retrieve features from DAS annotation servers.
- - Sequence ID Tooltip (application only)
-
This submenu's options allow the inclusion or exclusion of
- non-positional sequence features or database cross references
- from the tooltip shown when the mouse hovers over the sequence ID panel.
- - Alignment Properties...
- Displays some simple statistics computed for the
- current alignment view and any named properties defined on the
- whole alignment.
- - 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.
-
-
- Alignment Window Format Menu
-
- - Font...
- Opens the "Choose Font" dialog box, in order to
- change the font of the display and enable or disable 'smooth fonts'
- (anti-aliasing) for faster alignment rendering.
- - 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.
- Additional options for display of sequence numbering and scales are
- also visible in wrapped layout mode:
-
- - Scale Above
- Show the alignment column position scale.
- - Scale Left
- Show the sequence position for the first aligned residue in each row
- in the left column of the alignment.
- - Scale Right
- Show the sequence position for the last aligned residue in each row
- in the right-most column of the alignment.
- - Show Sequence Limits
- 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
- - Right Align Sequence ID
- If this box is selected then the sequence names displayed in
- the sequence label area will be aligned against the left-hand edge of
- the alignment display, rather than the left-hand edge of the alignment
- window.
- - Show Hidden Markers
- When this box is selected, positions in the alignment where
- rows and columns are hidden will be marked by blue arrows.
- - 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.
- - Centre Annotation Labels
- Select this to center labels along an annotation row
- relative to their associated column (default is off, i.e. left-justified).
- - Show Unconserved
- When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
-
-
-
- - 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
- Text...
- Opens the Colour Text dialog box to set a different text colour for
- light and dark background, and the intensity threshold for transition
- between them.
- - 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
+
+ - 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
+ Text...
Opens the Colour Text dialog box to
+ set a different text colour for light and dark background, and the
+ intensity threshold for transition between them.
+
+ - Colour Scheme options: None, ClustalX,
+ Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, 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.
+ - By RNA Helices
+ Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ RNA Helices
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 Length
This will
+ sort the sequences according to their length (excluding gap
+ characters). 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
+
+
+ Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.
+
+ - 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 similarity scores calculated with
+ the alignment. See Principal
+ Component Analysis.
+
+ - Extract Scores ... (optional)
This
+ option is only visible if Jalview detects one or more white-space
+ separated values in the description line of the alignment
+ sequences.
When selected, these numbers are parsed into
+ sequence associated annotation which can then be used to sort the
+ alignment via the Sort by→Score menu.
+
+ - Autocalculate Consensus
For
+ large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy
+ calculations performed after each sequence edit.
+
+ - Sort With New Tree
When
+ enabled, Jalview will automatically sort the alignment when a new
+ tree is calculated or loaded onto it.
+ - Show Flanking Regions
Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides.
+
+
+ - Web Service Menu
This menu
+ is dynamic, and may contain user-defined web service entries in
+ addition to any of the following ones:
+
+ - Fetch DB References
This
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+ - 'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment.
Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !
Added in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<
+
Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
+
+ 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.
+
+
+ - Alignment
Align the currently
+ selected sequences or all sequences in the alignment, or re-align
+ unaligned sequences to the aligned sequences. Entries in this menu
+ provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence
+ Alignment webservice client entry for more information.
+ - Secondary Structure Prediction
+
+ - JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. See
+ the Jpred3 client entry for
+ more information. 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 in the set
+ (that is, the one that appears first in the alignment window).
+
+
+
+ - Analysis
+
+ - Multi-Harmony
Performs
+ functional residue analysis on a protein family alignment with
+ sub-families defined on it. See the Multi-Harmony service entry for more
+ information.
+
+
+
-
- - 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 Length
- This will sort the sequences according to their length (excluding gap characters). 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.
-
- - Extract Scores ... (optional)
- This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
- When selected, these numbers are parsed into sequence associated annotation which can
- then be used to sort the alignment via the Sort by→Score menu.
-
- - Autocalculate Consensus
- For large alignments it can be useful to deselect
- "Autocalculate Consensus" when editing. This prevents the
- sometimes lengthy calculations performed after each sequence edit.
-
-
-
- - Web Service
-
- - Fetch DB References
- This will use any of the database services that Jalview is aware
- of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
- to verify the sequence and retrieve all database cross references and PDB ids
- associated with all or just the selected sequences in the alignment.
-
-
- 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.
- - MAFFT Multiple Sequence Alignment
- Submits all, or just the currently selected region for
- alignment with MAFFT.
- - Muscle Multiple Protein Sequence Alignment
- Submits all, or just 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 in the set (that is, the one
- that appears first in the alignment window).
-
-
-
-
-
+