Alignment Window Menus x
- 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
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.