#------------------------------------------------------------------------------- # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle # # This file is part of Jalview. # # Jalview is free software: you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. # # Jalview is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty # of MERCHANTABILITY or FITNESS FOR A PARTICULAR # PURPOSE. See the GNU General Public License for more details. # # You should have received a copy of the GNU General Public License along with Jalview. If not, see . #------------------------------------------------------------------------------- Alignment Window Menus

Alignment Window Menus

  • File
  • Edit
  • Select
  • View
  • Alignment Window Format Menu
    • Font...
      Opens the "Choose Font" dialog box, in order to change the font of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster alignment rendering.
    • Wrap
      When ticked, the alignment display is "wrapped" to the width of the alignment window. This is useful if your alignment has only a few sequences to view its full width at once.
      Additional options for display of sequence numbering and scales are also visible in wrapped layout mode:
      • Scale Above
        Show the alignment column position scale.
      • Scale Left
        Show the sequence position for the first aligned residue in each row in the left column of the alignment.
      • Scale Right
        Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.
      • Show Sequence Limits
        If this box is selected the sequence name will have the start and end position of the sequence appended to the name, in the format NAME/START-END
      • Right Align Sequence ID
        If this box is selected then the sequence names displayed in the sequence label area will be aligned against the left-hand edge of the alignment display, rather than the left-hand edge of the alignment window.
      • Show Hidden Markers
        When this box is selected, positions in the alignment where rows and columns are hidden will be marked by blue arrows.
      • Boxes
        If this is selected the background of a residue will be coloured using the selected background colour. Useful if used in conjunction with "Colour Text."
      • Text
        If this is selected the residues will be displayed using the standard 1 character amino acid alphabet.
      • Colour Text
        If this is selected the residues will be coloured according to the background colour associated with that residue. The colour is slightly darker than background so the amino acid symbol remains visible.
      • Show Gaps
        When this is selected, gap characters will be displayed as "." or "-". If unselected, then gap characters will appear as blank spaces.
        You may set the default gap character in preferences.
      • Centre Annotation Labels
        Select this to center labels along an annotation row relative to their associated column (default is off, i.e. left-justified).
      • Show Unconserved
        When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
    • 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, 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.
    • 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.
    • Web Service
      • 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.
      Selecting one of the following menu items starts a remote service on compute facilities at the University of Dundee. You need a continuous network connection in order to use these services through Jalview.
      • Alignment
        • ClustalW Multiple Sequence Alignment
          Submits all, or just the currently selected sequences for alignment with clustal W.
        • ClustalW Multiple Sequence Alignment Realign
          Submits the alignment or currently selected region for re-alignment with clustal W. Use this if you have added some new sequences to an existing alignment.
        • MAFFT Multiple Sequence Alignment
          Submits all, or just the currently selected region for alignment with MAFFT.
        • Muscle Multiple Protein Sequence Alignment
          Submits all, or just the currently selected sequences for alignment using Muscle. Do not use this if you are working with nucleic acid sequences.
      • Secondary Structure Prediction
        • JPred Secondary Structure Prediction
          Secondary structure prediction by network consensus. 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).