Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=60068a9887dba34c9e7cf49b2f5f53a6fdc15931;hp=aceabce6cff415f41d403479174de80961e2d074;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index aceabce..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,454 +1,657 @@ + Alignment Window Menus -

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. -
- HTML
  - Create a web page from your - alignment.
- EPS
  - Create an Encapsulated - Postscript file from your alignment.
- PNG
  - Create a Portable Network - Graphics file from your 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.
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.
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.
+ +
+ 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. +
+
HTML
+ Create a web page + from your alignment. +
+
EPS
+ Create an Encapsulated + Postscript file from your alignment. +
+
PNG
+ Create a Portable + Network Graphics file from your alignment. +
+
SVG
+ Create a Scalable + Vector Graphics file from your alignment for embedding + in web pages. +
+
BioJS
+ Create a BioJS MSA + Viewer HTML file from your 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.
+
Select Highlighted Columns
Selects + the columns currently highlighted as a result of a find, mouse + over, or selection event from a linked structure viewer or other + application. Modifiers will work on some platforms: ALT will add + all but the highlighted set to the column selection, and CTRL + (or META) will toggle the selection.
+
+
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.
+ +
+ +

-
- 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.
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Secondary Structure Prediction -
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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).
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-
-
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+ +
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 or PCA ...
Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region. +
+
Pairwise Alignments
Applies + Smith and Waterman algorithm to selected sequences. See pairwise + alignments. +
+
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 Jpred + 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 JPred 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 JPred 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 JPred 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. +
+
+
+
+