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-
-
Menus
-
-
-Alignment Menu
-
- - File
-
- - Save As
- 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.
-
- - Export
- Creates an alignment output maintaining the 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.
-
-
-
- - 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.
- Select the format of the text by selecting one of the following menu items.
-
- - FASTA
- - MSF
- - CLUSTAL
- - BLC
- - PIR
- - PFAM
-
-
-
- - Print
- Jalview will print the alignment using the current fonts and
- coloursof 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.
- - Load Associated Tree
- Jalview can load in trees which are in the Newick file format
- and associate them with a particular alignment. Note: the ids of the tree
- file and your alignment MUST be the same.
- - Close
- Close the alignment window. Be aware that changes to your alignment
- will not be save unless specifically actioned from the "Save As"
- menu.
-
-
- - Edit
-
-
-
- - 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, pasting
-
- - Redo
-
- - Cut
- - Copy
- - Paste
-
- - To New Alignment
- - Add To This Alignment
-
-
- - Delete
- - Select All
- - Deselect All
- - Invert Selection
- - Undefine Groups
- - Remove Left
- - Remove Right
- - Remove Empty Columns
- - Remove All Gaps
- - Remove Redundancy
- - Pad Gaps
-
-
-
-
-
-
-
-
-
- - Font
- - Wrap
- - Show Full Sequence ID
- - Boxes
- - Text
- - Colour Text
- - Show Gaps
- - Show Annotations
- - Sequence Features
- - Overview Window
-
-
-
-
-
- - Apply Colour To All Groups
- - None
- - ClustalX
- - Blosum62 Score
- - Percentage Identity
- - Zappo
- - Taylor
- - Hydrophobicity
- - Helix Propensity
- - Strand Propensity
- - Turn Propensity
- - Buried Index
- - Nucleotide
- - User Defined
- - By Conservation
- - Modify Conservation Threshold
- - Above Identity Threshold
- - Modify Identity Threshold
-
-
-
-
-
- - Sort
-
- - by ID
- - by Group
- - by Pairwise Identity
-
-
- - Calculate Tree
-
- - Average Distance Using % Identity
- - Neighbour Joining Using % Identity
- - Average Distance Using Blosum62
- - Neighbour Joining Using Blosum62
-
-
- - Paiwise Alignments
- - Principal Component Analysis
- - Web Service
-
- - Clustal Alignment
- - JPred
- - Muscle Alignment
-
-
-
-
-
-
-
+
+
+
+Alignment Window Menus
+
+
+
+
+
+ Alignment Window Menus
+
+
+ - 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
+ - PileUp
+ - AMSA
+ - STH
+ - Phylip
+ - JSON
+
+ - Page Setup ...
Open
+ the printing system's Page Setup dialog box, to control page
+ size, layout and orientation.
+ - 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 from the Desktop's Save
+ Project File menu option, 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 right of the rightmost 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 are no empty columns before or after the
+ first or last aligned residue) and all sequences will be
+ padded with gap characters 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.
+ - 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 at marked
+ columns.
+
+ - Undefine Groups (Control U)
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
+ - Select/Hide Columns by Annotation
Select
+ or Hide columns in the alignment according to secondary
+ structure, labels and values shown in alignment annotation
+ rows.
+
+ - 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 Sequence Features
Show
+ or hide sequence features on this alignment.
+ - Sequence 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.
+
+ - Annotations (Since Jalview 2.8.2)
+
+ - 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.
+ - Show Alignment Related
+ Show all annotations that are for the alignment as a whole
+ (for example, Consensus, or secondary structure prediction
+ from alignment).
+ - Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
+ - Show Sequence Related
+ Show all annotations that are for individual sequences.
+ - Hide Sequence Related
+ Hide all annotations that are for individual sequences.
+ - You can also selectively show or hide
+ annotations from the Popup or
+ Annotation menus.
+
+ - Sort by Sequence
Sort
+ sequence-specific annotations by sequence order in the
+ alignment (and within that, by label).
+ - Sort by Label
Sort
+ sequence-specific annotations by label (and within that, by
+ sequence order). If neither sort order is selected, no
+ sorting is applied, allowing you to make a manual ordering
+ of the annotations.
+ - Autocalculated Annotation
+ Settings for the display of autocalculated annotation.
+
+ - Show first
Show
+ autocalculated annotations above sequence-specific
+ annotations. Note this also applies to other annotations
+ for the alignment, for example secondary structure
+ prediction from alignment.
+ - Show last
Show
+ autocalculated / alignment annotations below
+ sequence-specific annotations.
+ - 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).
+ - Group Consensus
+ When ticked, display a consensus row for all
+ groups.
+
+
+ - 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, 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.
+
+
+ - Neighbour Joining Using PAM250
+ - Neighbour Joining Using Sequence
+ Feature Similarity
+ - Neighbour Joining Using Blosum62
+ - Neighbour Joining Using % Identity
+ - Average Distance Using PAM250
+ - Average Distance Using Sequence
+ Feature Similarity
+ - Average Distance Using Blosum62
+ - Average Distance Using % Identity
+
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.
+
+
+
+
+
+
+