X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5f60ba52d6323b95055ab6742350fe4fc583404d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d53b3eb799f7436865dd10a3e904bf9710db5549;hpb=bda1b6a4412a73727de4613cfe3a6829b0fe0804;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d53b3eb..5f60ba5 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,583 +1,678 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Alignment Window Menus -

- Alignment Window Menus -

- + -
  • 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, 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 .
       -
      • -
    • 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.
      • -
    • By RNA Helices
      - Colours the helices of an RNA alignment loaded from a Stockholm file. See - RNA Helices - 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.
      -
      • -
    • Sort With New Tree
      When - enabled, Jalview will automatically sort the alignment when a new - tree is calculated or loaded onto it.
      • -
    • +
  • 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, 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 + .
      +
      • +
    • 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. +
      • +
    • By RNA Helices
      Colours + the helices of an RNA alignment loaded from a Stockholm file. + See RNA + Helices 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. + +
        +
      • 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. +
      • +
    • 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 + large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This + prevents the sometimes lengthy calculations performed after + each sequence edit.
      • +
    • 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: -
      -
    • 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.
      'Standard Databases' will check - sequences against the EBI databases plus any active DAS sequence - sources, or you can verify against a specific source from one of - the sub-menus.
      • -
    • Envision2 Services
      Submits one or - more sequences, sequence IDs or database references to analysis - workflows provided by the EnVision2 web - application. This allows Jalview users to easily access the EnCore - network of databases and analysis services developed by members of - ENFIN.
      • -
    -

    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.
      • -
    • Secondary Structure Prediction -
        -
      • 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: -
          -
        • 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). -
          • -
        -
      • -
    • Analysis
      -
        -
      • 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. -
        • -
      • -
    • - +
  • Web Service Menu
    This menu + 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. +
      • +
    +

    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. +
      • +
    • Secondary Structure Prediction +
        +
      • 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: +
          +
        • 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). +
          • +
        +         +
      • +
    • Analysis
      +
        +
      • 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. +
        • +
      • +
    • +