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
- 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.
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
- 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.
- Sort With New Tree
When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.
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
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.
'Standard Databases' will check
sequences against the EBI databases plus any active DAS sequence
sources, or you can verify against a specific source from one of
the sub-menus.
- Envision2 Services
Submits one or
more sequences, sequence IDs or database references to analysis
workflows provided by the EnVision2 web
application. This allows Jalview users to easily access the EnCore
network of databases and analysis services developed by members of
ENFIN.
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.