X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5f60ba52d6323b95055ab6742350fe4fc583404d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ef2b98983413fce772f0c2f3a23ba981d641234d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ef2b989..5f60ba5 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,504 +1,678 @@ + * 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 +

        +
          +
        • 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
              • +
            • PileUp
              • +
            • AMSA
              • +
            • STH
              • +
            • Phylip
              • +
            • JSON
              • +
            • +
          • Page Setup ...
            Open + the printing system's Page Setup dialog box, to control page + size, layout and orientation.
            • +
          • 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 from the Desktop's Save + Project File menu option, 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 are no empty columns before or after the + first or last aligned residue) and all sequences will be + padded with gap characters 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.
            • +
          • 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 at marked + columns. +
            • +
          • Undefine Groups (Control U)
            +             The alignment will be reset with no defined groups.
            + WARNING: This cannot be undone. +
            • +
          • Select/Hide Columns by Annotation
            Select + or Hide columns in the alignment according to secondary + structure, labels and values shown in alignment annotation + rows.
            • +
          • +
        • 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 Sequence Features
            Show + or hide sequence features on this alignment.
            • +
          • Sequence 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.
            • +
          • +
        • Annotations (Since Jalview 2.8.2) +
            +
          • 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.
            • +
          • Show Alignment Related
            + Show all annotations that are for the alignment as a whole + (for example, Consensus, or secondary structure prediction + from alignment).
            • +
          • Hide Alignment Related
            + Hide all annotations that are for the alignment as a whole.
            • +
          • Show Sequence Related
            + Show all annotations that are for individual sequences.
            • +
          • Hide Sequence Related
            + Hide all annotations that are for individual sequences.
            • +
          • You can also selectively show or hide + annotations from the Popup or + Annotation menus. +
            • +
          • Sort by Sequence
            Sort + sequence-specific annotations by sequence order in the + alignment (and within that, by label).
            • +
          • Sort by Label
            Sort + sequence-specific annotations by label (and within that, by + sequence order). If neither sort order is selected, no + sorting is applied, allowing you to make a manual ordering + of the annotations.
            • +
          • Autocalculated Annotation
            +             Settings for the display of autocalculated annotation. +
              +
            • Show first
               Show + autocalculated annotations above sequence-specific + annotations. Note this also applies to other annotations + for the alignment, for example secondary structure + prediction from alignment.
              • +
            • Show last
               Show + autocalculated / alignment annotations below + sequence-specific annotations.
              • +
            • 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).
              • +
            • Group Consensus
              +               When ticked, display a consensus row for all + groups.
              • +
            • +
          • +
        • 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.
              • + +
            • +
          • + +
        • -
      - 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).
          • -
        -
        • -
      -
      • -
    + +
  • Colour +
      +
    • Apply Colour To All Groups
      +       If this is selected, any changes made to the background + colour will be applied to all currently defined groups.
      +
      • +
    • Colour Text...
      Opens the Colour Text + dialog box to set a different text colour for light and dark + background, and the intensity threshold for transition between + them.
      • +
    • Colour Scheme options: None, ClustalX, + Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn + Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User + Defined
      +       See colours + for a description of all colour schemes. +
      • +
    • By Conservation
      +       See Colouring + by Conservation. +
      • +
    • Modify Conservation Threshold
      +       Use this to display the conservation threshold slider + window. Useful if the window has been closed, or if the 'by + conservation' option appears to be doing nothing!
      • +
    • Above Identity Threshold
      +       See Above + Percentage Identity + .
      +
      • +
    • Modify Identity Threshold
      +       Use this to set the threshold value for colouring above + Identity. Useful if the window has been closed.
      +
      • +
    • By Annotation
      Colours + the alignment on a per-column value from a specified + annotation. See Annotation Colouring. +
      • +
    • By RNA Helices
      Colours + the helices of an RNA alignment loaded from a Stockholm file. + See RNA + Helices Colouring. +
      • +
    • +
  • Calculate +
      +
    • Sort +
        +
      • by ID
        This will + sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be + inverted.
        • +
      • by Length
        This + will sort the sequences according to their length + (excluding gap characters). If the sort is repeated, the + order of the sorted sequences will be inverted.
        • +
      • by Group
        This + will sort the sequences according to sequence name. If the + sort is repeated, the order of the sorted sequences will + be inverted.
        • +
      • by Pairwise Identity
        +         This will sort the selected sequences by their + percentage identity to the consensus sequence. The most + similar sequence is put at the top.
        • +
      • The Sort + menu will have some additional options if you have just + done a multiple alignment calculation, or opened a tree + viewer window. +
        • +
      • +
    • Calculate Tree
      Functions + for calculating trees on the alignment or the currently + selected region. See calculating + trees. + +
        +
      • Neighbour Joining Using PAM250
        • +
      • Neighbour Joining Using Sequence + Feature Similarity
        • +
      • Neighbour Joining Using Blosum62
        • +
      • Neighbour Joining Using % Identity
        • +
      • Average Distance Using PAM250
        • +
      • Average Distance Using Sequence + Feature Similarity
        • +
      • Average Distance Using Blosum62
        • +
      • Average Distance Using % Identity
        • +
      Note: Since Version 2.8.1, a number of + additional similarity measures for tree calculation are + provided in this menu.
      • +
    • Pairwise Alignments
      Applies + Smith and Waterman algorithm to selected sequences. See pairwise alignments. +
      • +
    • Principal Component Analysis
      Shows + a spatial clustering of the sequences based on similarity + scores calculated with the alignment. See Principal Component Analysis. +
      • +
    • Extract Scores ... (optional)
      This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
      When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
      • +
    • Autocalculate Consensus
      For + large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This + prevents the sometimes lengthy calculations performed after + each sequence edit.
      • +
    • Sort With New Tree
      When + enabled, Jalview will automatically sort the alignment when a + new tree is calculated or loaded onto it.
      • +
    • Show Flanking Regions
      Opens + a new alignment window showing any additional sequence data + either side of the current alignment. Useful in conjunction + with 'Fetch Database References' when the 'Trim Retrieved + Sequences' option is disabled to retrieve full length + sequences for a set of aligned peptides.
      • +
    • + +
  • Web Service Menu
    This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +
      +
    • Fetch DB References
      This + 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. +
        • +
      • +
    • + +