X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=966c0053a7e4ecfff93c1337c396ba6ddbbe66a0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=280cce99f626bd829a61e2706a7cdcd6441fef7c;hpb=8891eedbf7430d8a98edc1cccb32fceac8e3a9bb;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 280cce9..966c005 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,329 +1,620 @@ - -Menus - - -

Alignment Menu

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

+ Alignment Window Menus +

+ + + +
  • Colour +
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    • Apply Colour To All Groups
      If + this is selected, any changes made to the background colour will + be applied to all currently defined groups.
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      • +
    • 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 .
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      • +
    • Modify Identity Threshold
      Use + this to set the threshold value for colouring above Identity. + Useful if the window has been closed.
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      • +
    • 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.
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    • +
  • Calculate +
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    • Sort +
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      • 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.         +
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      • 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.
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      • 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.
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    • Calculate Tree
      Functions + for calculating trees on the alignment or the currently selected + region. See calculating + trees. +
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      • Average Distance Using % Identity
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      • Neighbour Joining Using % Identity
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      • Average Distance Using Blosum62
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      • Neighbour Joining Using Blosum62
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      + 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.
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    • Principal Component Analysis
      Shows + a spatial clustering of the sequences based on similarity scores calculated with + the alignment. See Principal + Component Analysis.
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      • +
    • 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.
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      • +
    • 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.
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      • +
    • 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: +
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    • 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. +
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      • '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. +

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    • 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 +
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      • 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: +
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        • 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). +
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      • +
    • Analysis
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      • 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. +
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    • + + + +