Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f3ab75dfbbc55786166c79c35ee50254ede337c9;hb=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=eb51c6268c863274f4a9454840c36820ee9e9fd7;hpb=8a6e4d35873d3e938a4e4d73467ffbd9b317f0d0;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index eb51c62..f3ab75d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,579 +1,653 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Alignment Window Menus -

- Alignment Window Menus -

File -
- Fetch Sequence
  Shows a - dialog window in which you can retrieve known ids from Uniprot, - EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the - European Bioinformatics Institute. See Sequence Fetcher .
- Add Sequences
  Add - sequences to the visible alignment from file, URL, or cut & - paste window -
- Reload
  Reloads the - alignment from the original file, if available.
  Warning: - This will delete any edits, analyses and colourings applied since - the alignment was last saved, and cannot be undone. -
- Save (Control S)
  Saves - the alignment to the file it was loaded from (if available), in - the same format, updating the original in place. -
- Save As (Control Shift S)
  Save - the alignment to local file. A file selection window will open, - use the "Files of type:" selection box to determine - which alignment format to save as. -
- Output to Textbox
  The - alignment will be displayed in plain text in a new window, which - you can "Copy and Paste" using the pull down menu, or - your standard operating system copy and paste keys. The output - window also has a "New Window" button - to import the (possibly edited) text as a new alignment.
  - Select the format of the text by selecting one of the following - menu items. -
  - FASTA -
  - MSF -
  - CLUSTAL -
  - BLC -
  - PIR -
  - PFAM -
- Print (Control P)
  Jalview - will print the alignment using the current fonts and colours of - your alignment. If the alignment has annotations visible, these - will be printed below the alignment. If the alignment is wrapped - the number of residues per line of your alignment will depend on - the paper width or your alignment window width, whichever is the - smaller. -
- Export Image
  Creates an - alignment graphic with the current view's annotation, alignment - background colours and group colours. If the alignment is wrapped, the output will also be - wrapped and will have the same visible residue width as the open - alignment. -
  - 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. -
- 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. -

-
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. -
+ +
+ 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.
+
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.
-
-
-
+
-
-
+
+
-
Colour -
-
Apply Colour To All Groups
If - this is selected, any changes made to the background colour will - be applied to all currently defined groups.
-
-
Colour - Text...
Opens the Colour Text dialog box to - set a different text colour for light and dark background, and the - intensity threshold for transition between them. -
-
Colour Scheme options: None, ClustalX, - Blosum62 Score, Percentage Identity, Zappo, Taylor, - Hydrophobicity, Helix Propensity, Strand Propensity, Turn - Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
See - colours for a - description of all colour schemes.
-
By Conservation
See Colouring by - Conservation.
-
Modify Conservation Threshold
Use - this to display the conservation threshold slider window. Useful - if the window has been closed, or if the 'by conservation' option - appears to be doing nothing!
-
Above Identity Threshold
See - Above Percentage - Identity .
-
-
Modify Identity Threshold
Use - this to set the threshold value for colouring above Identity. - Useful if the window has been closed.
-
-
By Annotation
Colours - the alignment on a per-column value from a specified annotation. - See Annotation - Colouring.
-
By RNA Helices
- Colours the helices of an RNA alignment loaded from a Stockholm file. See - RNA Helices - Colouring.
-
-
-
Calculate -
-
Sort -
-
by ID
This will sort - the sequences according to sequence name. If the sort is - repeated, the order of the sorted sequences will be inverted. -
-
by Length
This will - sort the sequences according to their length (excluding gap - characters). If the sort is repeated, the order of the sorted - sequences will be inverted.
-
by Group
This - will sort the sequences according to sequence name. If the sort - is repeated, the order of the sorted sequences will be inverted. -
-
by Pairwise Identity
This - will sort the selected sequences by their percentage identity to - the consensus sequence. The most similar sequence is put at the - top.
-
The Sort - menu will have some additional options if you have just done a - multiple alignment calculation, or opened a tree viewer window.
-
-
-
-
Calculate Tree
Functions - for calculating trees on the alignment or the currently selected - region. See calculating - trees. -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
-
-
-
-
Pairwise Alignments
Applies - Smith and Waterman algorithm to selected sequences. See pairwise alignments.
-
-
Principal Component Analysis
Shows - a spatial clustering of the sequences based on the BLOSUM62 scores - in the alignment. See Principal - Component Analysis.
-
-
Extract Scores ... (optional)
This - option is only visible if Jalview detects one or more white-space - separated values in the description line of the alignment - sequences.
When selected, these numbers are parsed into - sequence associated annotation which can then be used to sort the - alignment via the Sort by→Score menu.
-
-
Autocalculate Consensus
For - large alignments it can be useful to deselect "Autocalculate - Consensus" when editing. This prevents the sometimes lengthy - calculations performed after each sequence edit.
-
-
Sort With New Tree
When - enabled, Jalview will automatically sort the alignment when a new - tree is calculated or loaded onto it.
-
+
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: -
+
Web Service Menu
This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +

Fetch DB References
This - will use any of the database services that Jalview is aware of - (e.g. DAS sequence servers and the WSDBFetch service provided by - the EBI) to verify the sequence and retrieve all database cross - references and PDB ids associated with all or just the selected - sequences in the alignment.
'Standard Databases' will check - sequences against the EBI databases plus any active DAS sequence - sources, or you can verify against a specific source from one of - the sub-menus.
-
Envision2 Services
Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.
+ submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. those provided by + EMBL-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.
+
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. -
-
-
-
+
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. +
+
+
+