X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=a7cb733d856154ee6f042de9e3348951b309f245;hb=87fa9a883d14416ba0e7f778bad69de813048b9c;hp=1e1cfdc4b9fb14042b293bc8f3623bee1040474f;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 1e1cfdc..a7cb733 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,22 +1,24 @@ + --> Alignment Window Menus @@ -110,7 +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 @@ -283,6 +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. + 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 @@ -509,28 +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