Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=2a65e4319ab97b80da3bbab76b46f3b5cb9e4fb0;hb=67473776389cd0a6024aa3e401819e503970082c;hp=b3682357451635911f443402b2b211a6a03d6f1d;hpb=3e0eb5fe92f38828607594c7b70dfdf012e4d3dc;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index b368235..2a65e43 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,448 +1,639 @@ - - -Alignment Window Menus - + + + + 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.

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.
+ + +
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. +
+
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.
+
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. +
+ +

-
- 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).
-
-
-
-
+ +
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.
+ +
+
+ +
+
+ + + \ No newline at end of file