X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=3a057a8567b9f4801af371898373e9147a790ad5;hb=54cbe6eeaf683e042246c657716514d80e561a9c;hp=ce339cc6a52654ebc383f42f9e4dac38f6e5d12c;hpb=db098429f712e3cda729b937cd3f635482f96b52;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ce339cc..3a057a8 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -33,7 +33,7 @@
  • Select @@ -248,7 +244,7 @@ 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 @@ -278,11 +274,16 @@ 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.
    • + href="../features/columnFilterByAnnotation.html">Select/Hide + Columns by Annotation
    Select or Hide + columns in the alignment according to secondary structure, + labels and values shown in alignment annotation rows. +
  • Select Highlighted Columns
    Selects + the columns currently highlighted as a result of a find, mouse + over, or selection event from a linked structure viewer or other + application. Modifiers will work on some platforms: ALT will add + all but the highlighted set to the column selection, and CTRL + (or META) will toggle the selection.
  • View
    • @@ -474,11 +471,10 @@ 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.
    • + href="../colourSchemes/textcolour.html">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 @@ -487,7 +483,13 @@ See colours for a description of all colour schemes.
    • -
  • By Conservation
    +
  • Sequence ID
    Shades + sequences using their Sequence ID colour. Useful when + performing tree + based subfamily analysis. +
    • +
  • By Conservation
    See Colouring by Conservation.
    • @@ -507,8 +509,8 @@
  • By Annotation
    Colours the alignment on a per-column value from a specified annotation. See Annotation Colouring. + href="../colourSchemes/annotationColouring.html">Annotation + Colouring.
  • By RNA Helices
    Colours the helices of an RNA alignment loaded from a Stockholm file. @@ -542,44 +544,26 @@ 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. +
  • Calculate Tree or PCA ...
    Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region.
    • -
  • 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 +
  • Pairwise Alignments
    Applies + Smith and Waterman algorithm to selected sequences. See pairwise + alignments. +
    • +
  • 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 @@ -599,63 +583,60 @@ 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. -
      • -
    +
  • Fetch DB References
    This + submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. those provided by + EMBL-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.
      • +
    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. +
    • 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 + consensus. See the Jpred 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 + sequences appear to be aligned, then a JPred 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 + the automatic JPred 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 + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
          • @@ -667,8 +648,8 @@
        • 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. + href="../webServices/shmr.html">Multi-Harmony + service entry for more information.