X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=2a65e4319ab97b80da3bbab76b46f3b5cb9e4fb0;hb=67473776389cd0a6024aa3e401819e503970082c;hp=ef2b98983413fce772f0c2f3a23ba981d641234d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ef2b989..2a65e43 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,504 +1,639 @@ - + + - -Alignment Window Menus - + * 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 - -
    • -
  • Edit - -
    • -
  • Select - -
    • -
  • View - -
    • -
  • 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.
        + + +

        Alignment Window Menus x

        + +
          + +
        • 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. +
            • + +
          • -
        - 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).
            • -
          -
          • -
        -
        • + +
      • Alignment Window Format Menu +
          + +
        • Font...
          +           Opens the "Choose Font" dialog box, in order to +change the font of the display and enable or disable 'smooth fonts' +(anti-aliasing) for faster alignment rendering.
          • + +
        • Wrap
          +           When ticked, the alignment display is "wrapped" to the width of the +alignment window. This is useful if your alignment has only a few +sequences to view its full width at once.
          +Additional options for display of sequence numbering and scales are +also visible in wrapped layout mode:
          +           +
            + +
          • Scale Above
            + Show the alignment column position scale.
            • + +
          • Scale Left
            + Show the sequence position for the first aligned +residue in each row in the left column of the alignment.
            • + +
          • Scale Right
            + Show the sequence position for the last aligned +residue in each row in the right-most column of the alignment.
            • + +
          • Show Sequence Limits
            +             If this box is selected the sequence name will +have the start and end position of the sequence appended to the name, +in the format NAME/START-END
            • + +
          • Right Align Sequence ID
            +             If this box is selected then the sequence +names displayed in the sequence label area will be aligned against the +left-hand edge of the alignment display, rather than the left-hand edge +of the alignment window.
            • + +
          • Show Hidden Markers
            +             When this box is selected, positions in the +alignment where rows and columns are hidden will be marked by blue +arrows.
            • + +
          • Boxes
            +If this is selected the background of a residue will be coloured using +the selected background colour. Useful if used in conjunction with +"Colour Text."
            • + +
          • Text
            +             If this is selected the residues will be +displayed using the standard 1 character amino acid alphabet.
            • + +
          • Colour Text
            +             If this is selected the residues will be +coloured according to the background colour associated with that +residue. The colour is slightly darker than background so the amino +acid symbol remains visible.
            • + +
          • Show Gaps
            +             When this is selected, gap characters will be +displayed as "." or "-". If unselected, then gap characters will appear +as blank spaces.
            +You may set the default gap character in preferences.
            • + +
          • Centre Annotation Labels
            +             Select this to center labels along an +annotation row relative to their associated column (default is off, +i.e. left-justified).
            • + +
          • Show Unconserved
            +             When this is selected, all consensus sequence +symbols will be rendered as a '.', highlighting mutations in highly +conserved alignments.
            • + +
          +
          • + +
        +
        • +
      - - + + +
    • Colour +
        + +
      • Apply Colour To All Groups
        +         If this is selected, any changes made to the +background colour will be applied to all currently defined groups.
        +
        • + +
      • Colour +Text...
        +Opens the Colour Text dialog box to set a different text colour for +light and dark background, and the intensity threshold for transition +between them.
        • + +
      • Colour Scheme options: None, ClustalX, +Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, +Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, +Nucleotide, Purine/Pyrimidine, User Defined
        +         See colours +for a description of all colour schemes.
        +
        • + +
      • By Conservation
        +         See Colouring +by Conservation.
        +
        • + +
      • Modify Conservation Threshold
        +         Use this to display the conservation threshold +slider window. Useful if the window has been closed, or if the 'by +conservation' option appears to be doing nothing!
        +
        • + +
      • Above Identity Threshold
        +         See Above +Percentage Identity .
        +
        • + +
      • Modify Identity Threshold
        +         Use this to set the threshold value for colouring +above Identity. Useful if the window has been closed.
        +
        • + +
      • By Annotation
        + Colours the alignment on a per-column value from a specified +annotation. See Annotation +Colouring.
        +
        • + +
      • By RNA Helices
        + Colours the helices of an RNA alignment loaded from a +Stockholm file. See RNA +Helices Colouring.
        +
        • + +
      +
      • + + +
    • Calculate +
        + +
      • Sort +
          + +
        • by ID
          +This will sort the sequences according to sequence name. If the sort is +repeated, the order of the sorted sequences will be inverted.
          • + +
        • by Length
          +This will sort the sequences according to their length (excluding gap +characters). If the sort is repeated, the order of the sorted sequences +will be inverted.
          • + +
        • by Group
          +           This will sort the sequences according to +sequence name. If the sort is repeated, the order of the sorted +sequences will be inverted.
          • + +
        • by Pairwise Identity
          +           This will sort the selected sequences by their +percentage identity to the consensus sequence. The most similar +sequence is put at the top.
          • + +
        • The Sort +menu will have some additional options if you have just done a +multiple alignment calculation, or opened a tree viewer window.
          +
          • + +
        +
        • + +
      • Calculate Tree
        + 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
          +
          • + +
        + 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 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.
          • + +
        +
        • + +
      +
      • + + + \ No newline at end of file