X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f23c1b76d378fec01f1c1ee5de8fc08b10edc403;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=427ab2d592a782f6e34c11f9ad1ec7b32b14fc9c;hpb=b64d78cc81a4d3f87ac03b4f530757b840c4f943;p=jalview.git
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-
-
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.
-
-
- - 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 select known ids from
+ Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+ the European Bioinformatics Institute. See Sequence Fetcher.
+ - Add Sequences
+ Add sequences to the visible alignment from file, URL, or cut &
+ paste window
+ - Reload
+ Reloads the alignment from the original file, if available.
+ Warning: This will delete any edits, analyses and
+ colourings applied since the alignment was last saved, and cannot be
+ undone.
+ - Save (Control S)
+ Saves the alignment to the file it was loaded from (if available), in
+ the same format, updating the original in place.
+ - Save As (Control Shift S)
+ Save the alignment to local file. A file selection window
+ will open, use the "Files of type:" selection box to
+ determine which alignment format to
+ save as.
+ - Output to Textbox
+ The alignment will be displayed in plain text in a new
+ window, which you can "Copy and Paste" using the pull down
+ menu, or your standard operating system copy and paste keys. The
+ output window also has a "New Window"
+ button to import the (possibly edited) text as a new alignment.
+ Select the format of the text by selecting one of the following menu
+ items.
+
+ - FASTA
+ - MSF
+ - CLUSTAL
+ - BLC
+ - PIR
+ - PFAM
+
+
+ - Print (Control P)
+ Jalview will print the alignment using the current fonts and
+ colours of your alignment. If the alignment has annotations visible,
+ these will be printed below the alignment. If the alignment is wrapped
+ the number of residues per line of your alignment will depend on the
+ paper width or your alignment window width, whichever is the smaller.
+
+ - Export Image
+ Creates an alignment graphic with the current view's annotation,
+ alignment background colours and group colours. If the alignment is wrapped, the output will also be
+ wrapped and will have the same visible residue width as the open
+ alignment.
+
+
+ - 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 Profile
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ -
+ 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:
+
+ - 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, 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 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.
+
+
+
+ - Web Service
+
+ - Fetch DB References
+ This will use any of the database services that Jalview is aware
+ of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
+ to verify the sequence and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+
+ Selecting one of the following menu items starts a remote
+ service on compute facilities at the University of Dundee. You need a
+ continuous network connection in order to use these services through
+ Jalview.
+
+ - Alignment
+
+ - ClustalW Multiple Sequence Alignment
+ Submits all, or just the currently selected sequences for
+ alignment with clustal W.
+ - ClustalW Multiple Sequence Alignment
+ Realign
+ Submits the alignment or currently selected region for
+ re-alignment with clustal W. Use this if you have added some new
+ sequences to an existing alignment.
+ - MAFFT Multiple Sequence Alignment
+ Submits all, or just the currently selected region for
+ alignment with MAFFT.
+ - Muscle Multiple Protein Sequence Alignment
+ Submits all, or just the currently selected sequences for
+ alignment using Muscle. Do not use this if you are working with
+ nucleic acid sequences.
+
+
+ - Secondary Structure Prediction
+
+ - JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. The
+ behaviour of this calculation depends on the current selection:
+ - If nothing is selected, and the displayed sequences
+ appear to be aligned, then a JNet prediction will be run for the
+ first sequence in the alignment, using the current alignment.
+ Otherwise the first sequence will be submitted for prediction.
+ - If just one sequence (or a region on one sequence)
+ has been selected, it will be submitted to the automatic JNet
+ prediction server for homolog detection and prediction.
+ - If a set of sequences are selected, and they appear
+ to be aligned, then the alignment will be used for a Jnet prediction
+ on the first sequence in the set (that is, the one
+ that appears first in the alignment window).
+
+
+
+
+
+
+