X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=ef2b98983413fce772f0c2f3a23ba981d641234d;hpb=247b4f59aad27b654fb55268b55645dc6496f12e;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ef2b989..e18e273 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -15,490 +15,4 @@ * 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

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  • File - -
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  • Edit - -
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  • Select - -
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  • View - -
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  • Alignment Window Format Menu -
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    • 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.
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    • 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:
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      • Scale Above
        - Show the alignment column position scale.
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      • Scale Left
        - Show the sequence position for the first aligned residue in each row - in the left column of the alignment.
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      • 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
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      • 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.
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      • Show Hidden Markers
        -         When this box is selected, positions in the alignment where - rows and columns are hidden will be marked by blue arrows.
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      • 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."
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      • Text
        -         If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
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      • 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.
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      • 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.
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      • Centre Annotation Labels
        -         Select this to center labels along an annotation row - relative to their associated column (default is off, i.e. left-justified).
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      • Show Unconserved
        -         When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. -
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    • 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.
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      • 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.
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      • By Conservation
        -         See Colouring - by Conservation.
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      • 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!
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      • 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.
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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.
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        • 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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      • 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 the - BLOSUM62 scores in 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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    • 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.
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        • -
      - 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. -
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      • Alignment -
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        • ClustalW Multiple Sequence Alignment
          - Submits all, or just the currently selected sequences for - alignment with clustal W.
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        • 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.
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        • 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.
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      • Secondary Structure Prediction -
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        • JPred Secondary Structure Prediction
          - Secondary structure prediction by network consensus. 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.
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        • 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.
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        • 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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