X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=9317de4ce997ec39dee25ec507c12807c5067d7d;hp=5739797abf93d7d68894458feb3f12d3ad6ebda3;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 5739797..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -133,10 +133,9 @@
  • Load Features / Annotations
    Load files describing precalculated sequence features or alignment annotations. + href="../features/featuresFormat.html">sequence + features or alignment + annotations.
  • Close (Control W)
    Close the alignment window. Make sure you have saved your @@ -204,16 +203,14 @@ All columns which only contain gap characters ("-", ".") will be deleted.
    You may set the default gap character in preferences. + href="../features/preferences.html">preferences.
  • Remove All Gaps (Control Shift E)
    Gap characters ("-", ".") will be deleted from the selected area of the alignment. If no selection is made, ALL the gaps in the alignment will be removed.
    You may set the default gap character in preferences. + href="../features/preferences.html">preferences.
  • Remove Redundancy (Control D)
    Selecting this option brings up a window asking you to @@ -233,8 +230,7 @@ with alignment analysis programs which require 'properly aligned sequences' to be all the same length.
    You may set the default for Pad Gaps in the preferences. + href="../features/preferences.html">preferences.
  • 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 +473,10 @@ 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 @@ -507,8 +505,8 @@
  • 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 +540,26 @@ 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 @@ -615,7 +595,7 @@ in Jalview 2.8.1
  • 'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources<
    • + 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. @@ -626,36 +606,35 @@ 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 +646,8 @@
        • 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.