Alignment Window Menus
---
-- 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 is a tab separated list:
--NAME START_RES END_RES SEQUENCE -
-- 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 Selection
-
- Any sequence ids currently not selected will replace the current - 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
-
- All gap characters ("-", ".") will be deleted from - the alignment.
- 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
-
- Adds gaps to the end of all the sequences so they - are all the same length. This is useful for making a tree using - unaligned sequences.
- You may set the default gap character in preferences. -
---
-- Find
-
- Select this to search - for residues, sequence name or residue position within the alignment.
---
+ +- Font
-
- Change the font of the display from the - "Choose Font" dialog box, which is shown when this - item is selected.
-- 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.
-- 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.
+- 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.- 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
+
+ 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.- 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 Selection
+
+ Any sequence ids currently not selected will replace the + current 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.- 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.
---
-- Apply Colour To All Groups
- If this is selected, any changes made to the background colour - will be applied to all currently defined groups.
+- 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.
- 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.
--
+ +- Sort -
-
- The Sort menu will - have some additional options if you have just done a multiple - alignment calculation, or opened a tree viewer window.- 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.
-
+- 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 Tree -
+
Functions for calculating trees on the alignment or the - currently selected region. See +- 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. -
-- 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. - --
+- Clustal Alignment
-
- Submits all, or just the currently selected sequences for alignment with clustal W.- Clustal 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 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.
-- JPred
+
- 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). -
- +- 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).
+-