Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=acf6d0deb9caf0148791f2993be0a2cd7987f569;hp=427ab2d592a782f6e34c11f9ad1ec7b32b14fc9c;hpb=b64d78cc81a4d3f87ac03b4f530757b840c4f943;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 427ab2d..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,365 +1,657 @@ - -Alignment Window Menus - - -

Alignment Window Menus

File -
- Add Sequences
  - Add sequences to the visible alignment from file, URL, or cut & paste - window
- 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.
- Save As
  - 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.
- Export
  - Creates an alignment graphic with the current 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.
  -
- 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.
  - Select the format of the text by selecting one of the following menu items. -
  - FASTA
  - MSF
  - CLUSTAL
  - BLC
  - PIR
  - PFAM
  -
- Print
  - 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 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
  - 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
  - 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
  - Any actions which you undo can be redone using redo.
- Cut
  - 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
  - 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
    - A new alignment window will be created from sequences - previously copied or cut to the system clipboard.
    - Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
  - Add To This Alignment
    - Copied sequences from another alignment window can be - added to the current Jalview alignment.
  -
- Delete
  - This will delete the currently selected residues without - copying them to the clipboard. Like the other edit operations, this can - be undone with Undo.
- Select All
  - Selects all the sequences and residues in the alignment. -
  - Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
- Deselect All
  - 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
  - Any sequence ids currently not selected will replace the - current selection.
- Invert Column Selection
  - Any columns currently not selected will replace the current - column selection.
- Undefine Groups
  - The alignment will be reset with no defined groups.
  - WARNING: This cannot be undone.
- Remove Left
  - 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
  - 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
  - All columns which only contain gap characters ("-", - ".") will be deleted.
  - You may set the default gap character in preferences. -
- Remove All Gaps
  - 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
  - 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. -
  -
-
Search -
- Find
  - Select this to search - for residues, sequence name or residue position within the alignment and - create new sequence features from the queries.
  -
-
View -
- Font
  - Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
- Smooth Fonts
  - If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
- Show (all Columns / Sequences)
  - All hidden Columns / Sequences will be revealed.
- Hide (all Columns / Sequences)
  - Hides the all the currently selected Columns / Sequences
- 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.
  - Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each - sequence row.
  - NOTE: When in wrapped alignment view, the alignment cannot - be edited or have regions selected on it.
- Show Full Sequence ID
  - 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
- 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.
- 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.
- Fetch Sequence Features
  - If the sequence names are Swissprot entries Jalview will - use the names to retrieve sequence - features from the EBI. Features which are 1 residue in length are - coloured red, sequences longer than 1 residue are coloured blue. Move - the mouse over a coloured feature to display the details of the feature. -
  - Note: The retrieved information will update the sequence start and end - labels if they are incorrect.
- Show Sequence Features
  - Show or hide sequence features on this alignment.
- Seqence Feature Settings...
  - Control the colour and display of sequence features on the alignment. - See Sequence Feature Settings.
- 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.
-
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 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.
- Translate cDNA
  - If you are viewing a cDNA alignment a very simple translation service - is available. The translation ignores all gaps in the cDNA sequences. -
  -
-
Web Service
- 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.
  - Muscle Multiple Protein Sequence Alignment
    - Submits all, or jut 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 selected in the set (that is, the one that was first clicked - on).
  -
-

- - + + + +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
  - 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.
+
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. +

+ + +