X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=c8b2270d685a9d8c1f79904818397452f96827fc;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=d53b3eb799f7436865dd10a3e904bf9710db5549;hpb=bda1b6a4412a73727de4613cfe3a6829b0fe0804;p=jalview.git
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+ * 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.
-
- - 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.
-
-
- - 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:
-
+
-
-
+
+
- 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
Functions
+ for calculating trees on the alignment or the currently
+ selected region. See calculating
+ trees.
+
+
+ - Neighbour Joining Using PAM250
+ - Neighbour Joining Using Sequence
+ Feature Similarity
+ - Neighbour Joining Using Blosum62
+ - Neighbour Joining Using % Identity
+ - Average Distance Using PAM250
+ - Average Distance Using Sequence
+ Feature Similarity
+ - Average Distance Using Blosum62
+ - Average Distance Using % Identity
+
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
- 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.
-
- 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.
-
-
-
-
+ 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.
+
+
+
+