Alignment Window Menus
File
- 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.
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.
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)
All hidden Columns / Sequences will be revealed.
- Hide→(all Columns / Sequences)
Hides the all the currently selected Columns / Sequences
- 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.
- 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.
- 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.
- 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).
- 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
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 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).