From 5a6d8d69732445af2189fc4bab7a09dbd77bb829 Mon Sep 17 00:00:00 2001
From: jprocter Colour schemes Jalview allows the user to set a background colour for the whole alignment
- and also set the colour of defined groups within the alignment. To change the background colour, simply select the colour from the "Colour"
- menu. To change the colour of a group, right click on any residue within a group
- and use the popup menu to define the group colour. At the top of the "Colour" menu the tick box "Apply Background
- Colour to all groups". This is automatically ticked as default and means
- the chosen colour will be applied to all existing groups. If you wish to maintain
- the colour scheme for defined groups, make sure you deselect this option before
- changing the background colour. Colour schemes Jalview allows the user to set a background colour for the whole
+alignment view or for each group defined on regions within it. To change the background colour, simply select the colour from
+the "Colour" menu. To change the colour of a group, right click on any residue
+within a group and use the popup menu to define the group colour. At the top of the "Colour" menu the tick box
+"Apply Background Colour to all groups". This is ticked by
+default so that a chosen colour scheme will be applied to all existing
+groups. If you wish to maintain the colour scheme for defined groups,
+make sure you deselect this option before changing the background
+colour. The "Colour→Colour Text..." entry
+opens a dialog box to set a different text colour for light and dark
+background, and the intensity threshold for transition between them. The default colour schemes are summarised in the table below:
+ Alignment Window Menus Alignment Window Menus Alignment Window Calculate Menu Alignment Window Calculate Menu
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- A
- R
- N
- D
- C
- Q
- E
- G
- H
- I
- L
- K
- M
- F
- P
- S
- T
- W
- Y
- V
- B
- X
- Z
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- Clustal
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- Hydrophobicity
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- Helix Propensity
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- Strand Propensity
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- Buried Index
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+ A
+ R
+ N
+ D
+ C
+ Q
+ E
+ G
+ H
+ I
+ L
+ K
+ M
+ F
+ P
+ S
+ T
+ W
+ Y
+ V
+ B
+ X
+ Z
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+ Clustal
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+ Zappo
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+ Taylor
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+ Hydrophobicity
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+ Helix Propensity
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+ Strand Propensity
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+ Turn Propensity
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+ Buried Index
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-
-
- Add sequences to the visible alignment from file, URL, or cut & paste
- window
- 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 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.
- 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.
-
-
-
- Create a web page from
- your alignment.
- Create an Encapsulated Postscript
- file from your alignment.
- Create a Portable Network
- Graphics file from your alignment.
- 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.
-
-
-
- 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.
- All features visible on the alignment can be saved to file or displayed
- in a textbox in either Jalview or GFF format
- All annotations visible on the alignment can be saved to file or displayed
- in a textbox in Jalview annotations format.
- 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 files describing precalculated sequence
- features or alignment
- annotations.
- 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.
-
-
-
- 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.
- Any actions which you undo can be redone using redo.
- 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.
- 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.
-
-
- 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.
- Copied sequences from another alignment window can be
- added to the current Jalview alignment.
- This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations, this can
- be undone with Undo.
- Selects all the sequences and residues in the alignment.
-
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select 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.
- Any sequence ids currently not selected will replace the
- current selection.
- Any columns currently not selected will replace the current
- column selection.
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.
- 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.
- 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.
- All columns which only contain gap characters ("-",
- ".") will be deleted.
- You may set the default gap character in preferences.
-
- 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.
-
- 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.
- 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 this to search
- for residues, sequence name or residue position within the alignment and
- create new sequence features from the queries.
-
-
-
- Change the font of the display from the "Choose Font"
- dialog box, which is shown when this item is selected.
- If selected, the alignment will be drawn with anti-aliasing on which looks
- better, but performace is reduced.
- All hidden Columns / Sequences will be revealed.
- Hides the all the currently selected Columns / Sequences
- 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.
- 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
- 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."
- If this is selected the residues will be displayed using
- the standard 1 character amino acid alphabet.
- 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.
- 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.
- 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.
- 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 or hide sequence features on this alignment.
- Control the colour and display of sequence features on the alignment.
- See Sequence Feature Settings.
- 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.
-
-
- If this is selected, any changes made to the background colour
- will be applied to all currently defined groups.
- See colours for
- a description of all colour schemes.
- See Colouring
- by Conservation.
- 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!
- See Above Percentage
- Identity.
- Use this to set the threshold value for colouring above Identity.
- Useful if the window has been closed.
- Colours the alignment on a per-column value from a specified annotation.
- See Annotation Colouring.
-
-
-
-
-
- This will sort the sequences according to sequence name. If the sort
- is repeated, the order of the sorted sequences will be inverted.
- This will sort the sequences according to sequence name.
- If the sort is repeated, the order of the sorted sequences will be
- inverted.
- This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put
- at the top.
- Functions for calculating trees on the alignment or the currently
- selected region. See calculating trees.
-
-
-
- Applies Smith and Waterman algorithm to selected sequences. See pairwise
- alignments.
- Shows a spatial clustering of the sequences based on the BLOSUM62
- scores in the alignment. See Principal
- Component Analysis.
- If you are viewing a cDNA alignment a very simple translation service
- is available. The translation ignores all gaps in the cDNA sequences.
-
-
- 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.
-
-
-
-
-
- Submits all, or just the currently selected sequences for alignment
- with clustal W.
- 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.
- 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 by network consensus. The behaviour
- of this calculation depends on the current selection:
+
+
+
diff --git a/help/html/menus/alwSelect.html b/help/html/menus/alwSelect.html
index 87b0a49..7c5085a 100644
--- a/help/html/menus/alwSelect.html
+++ b/help/html/menus/alwSelect.html
@@ -7,8 +7,9 @@ Alignment Window Menus
+
+
+ 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 to the visible alignment from file, URL, or cut &
+ paste window
+ 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.
+ Saves the alignment to the file it was loaded from (if available), in
+ the same format, updating the original in place.
+ 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.
+ 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.
+
+
+
+ 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.
+
+ 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.
+
+
+
+ Create a web page from your
+ alignment.
+ Create an Encapsulated
+ Postscript file from your alignment.
+ Create a Portable Network
+ Graphics file from your alignment.
+ All features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format
+ All annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format.
+ 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 files describing precalculated sequence features or alignment annotations.
+ 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.
+
+
+ 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.
+ Any actions which you undo can be redone using redo.
+ 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.
+ 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.
+
+
+ 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.
+ Copied sequences from another alignment window can be added
+ to the current Jalview alignment.
+ This will delete the currently selected residues without
+ copying them to the clipboard. Like the other edit operations, this
+ can be undone with Undo.
+ 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.
+ 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.
+ All columns which only contain gap characters ("-",
+ ".") will be deleted.
+ You may set the default gap character in preferences.
+ 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.
+ 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.
+ 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.
+
+
+ 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.
+ Selects all the sequences and residues in the alignment.
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
+ 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.
+ Any sequence ids currently not selected will replace the
+ current selection.
+ Any columns currently not selected will replace the current
+ column selection.
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
+
+ Creates a new view from the current alignment view.
+ Display each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously.
+ Each view associated with the alignment will be displayed within its
+ own tab on the current alignment window.
+ All hidden Columns / Sequences will be revealed.
+ Hides the all the currently selected Columns / Sequences
+ 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 or hide sequence features on this alignment.
+ 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.
+ 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.
+
+
+ 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.
+ 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:
+
+
+ Show the alignment column position scale.
+ Show the sequence position for the first aligned residue in each row
+ in the left column of the alignment.
+ Show the sequence position for the last aligned residue in each row
+ in the right-most column of the alignment.
+ 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
+ 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.
+ When this box is selected, positions in the alignment where
+ rows and columns are hidden will be marked by blue arrows.
+ 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."
+ If this is selected the residues will be displayed using the
+ standard 1 character amino acid alphabet.
+ 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.
+ 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.
+
+
+ If this is selected, any changes made to the background
+ colour will be applied to all currently defined groups.
+
+ 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.
+ See colours for a
+ description of all colour schemes.
+
+ See Colouring
+ by Conservation.
+
+ 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!
+
+ See Above
+ Percentage Identity.
+
+ Use this to set the threshold value for colouring above
+ Identity. Useful if the window has been closed.
+
+ Colours the alignment on a per-column value from a specified
+ annotation. See Annotation
+ Colouring.
+
+
+
+
+
+ This will sort the sequences according to sequence name. If the sort
+ is repeated, the order of the sorted sequences will be inverted.
+ This will sort the sequences according to sequence name. If
+ the sort is repeated, the order of the sorted sequences will be
+ inverted.
+ This will sort the selected sequences by their percentage
+ identity to the consensus sequence. The most similar sequence is put
+ at the top.
+
+ Functions for calculating trees on the alignment or the
+ currently selected region. See calculating
+ trees.
+
+
+
+
+ Applies Smith and Waterman algorithm to selected sequences.
+ See pairwise alignments.
+
+ Shows a spatial clustering of the sequences based on the
+ BLOSUM62 scores in the alignment. See Principal Component Analysis.
+
+ For large alignments it can be useful to deselect
+ "Autocalculate Consensus" when editing. This prevents the
+ sometimes lengthy calculations performed after each sequence edit.
+
+ 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.
+
+
+
+
+
+ Submits all, or just the currently selected sequences for
+ alignment with clustal W.
+ 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.
+ Submits all, or just the currently selected region for
+ alignment with MAFFT.
+ 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 by network consensus. The
+ behaviour of this calculation depends on the current selection:
- Opens the Find dialog box to perform regular expression searches on the
- aligned sequences and their IDs and create new features.
+ 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.
Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
-
-
+
+
-
-
- This will sort the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted.
- This will sort the sequences according to sequence name.
- If the sort is repeated, the order of the sorted sequences will be inverted.
-
- This will sort the selected sequences by their percentage
- identity to the consensus sequence. The most similar sequence is put at
- the top.
-
- Functions for calculating trees on the alignment or the currently selected
- region. See calculating trees.
-
-
-
-
- Applies Smith and Waterman algorithm to selected sequences. See pairwise
- alignments.
-
- Shows a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See Principal Component
- Analysis.
-
- For large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents lengthy calculations which are
- performed after each sequence edit.
-
+
+
+
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index ca8f81b..2d341fa 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -35,7 +35,6 @@
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.
+
+
+ This will sort the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be inverted.
+ This will sort the sequences according to sequence name.
+ If the sort is repeated, the order of the sorted sequences will be inverted.
+
+ This will sort the selected sequences by their percentage
+ identity to the consensus sequence. The most similar sequence is put at
+ the top.
+
+ Functions for calculating trees on the alignment or the currently selected
+ region. See calculating trees.
+
+
+
+
+ Applies Smith and Waterman algorithm to selected sequences. See pairwise
+ alignments.
+
+ Shows a spatial clustering of the sequences based on the BLOSUM62 scores
+ in the alignment. See Principal Component
+ Analysis.
+
+ For large alignments it can be useful to deselect "Autocalculate
+ Consensus" when editing. This prevents the sometimes lengthy calculations
+ performed after each sequence edit.
+
Desktop Menus
-diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index c99b64c..7dd7b40 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -1,63 +1,74 @@ - -
- -
-