X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=4a1a200377de05d2c1849d08be7d1aace67497f3;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=9fb408d8e7c7c15f214b3d6a6efc928fe7562966;hpb=1b81a47f3b7e3e68256dfc4367ec27adb2302e4c;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 9fb408d..4a1a200 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,354 +1,575 @@ - -Alignment Window Menus - - -

Alignment Window Menus

- - - + + + +Alignment Window Menus + + + +

+ Alignment Window Menus +

+ + + +
  • 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
        +
        • +
      +
      • +
    • 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.
      +
      • +
    • Sort With New Tree
      When + enabled, Jalview will automatically sort the alignment when a new + tree is calculated or loaded onto it.
      • +
    • + +
  • 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.
      • +
    +

    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. +
        • +
      • +
    • + + + +