X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=a7cb733d856154ee6f042de9e3348951b309f245;hb=87fa9a883d14416ba0e7f778bad69de813048b9c;hp=eb51c6268c863274f4a9454840c36820ee9e9fd7;hpb=8a6e4d35873d3e938a4e4d73467ffbd9b317f0d0;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index eb51c62..a7cb733 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,21 +1,24 @@ + * 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 @@ -109,7 +112,7 @@
  • Load Associated Tree
    Jalview can view trees - stored in the Newick file format, and associate them with the + 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 @@ -235,17 +238,21 @@ Any columns currently not selected will replace the current column selection.
    • -
  • Undefine Groups (Control U)
    The - alignment will be reset with no defined groups.
    WARNING: - This cannot be undone.     -
    • -
  • Make Groups
     The currently +
  • 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)
      @@ -278,6 +285,11 @@ conservation calculation, quality calculation and consensus values as bar charts.
      • +
    • Show All Annotations
      + Show all available annotations on the alignment. You can selectively hide these from the Popup + or Annotation menus. (Since Jalview 2.8.2)
      • +
    • Hide All Annotations
      + Hide all annotations on the alignment. (Since Jalview 2.8.2)
    • Autocalculated Annotation
      Settings for the display of autocalculated annotation.
        @@ -303,7 +315,7 @@
      • Show Sequence Features
        Show or hide sequence features on this alignment.
        • -
      • Seqence +
      • 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 @@ -479,14 +491,15 @@
      • 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 the BLOSUM62 scores - in the alignment. See Principal + a spatial clustering of the sequences based on similarity scores calculated with + the alignment. See Principal Component Analysis.
    • Extract Scores ... (optional)
      This @@ -504,28 +517,36 @@
    • 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 - 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.
      'Standard Databases' will check - sequences against the EBI databases plus any active DAS sequence - sources, or you can verify against a specific source from one of - the sub-menus.
      • -
    • Envision2 Services
      Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.
      • + 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