<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows
a dialog window in which you can retrieve known ids from
- Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
Web Services provided by the European Bioinformatics
Institute. See <a href="../features/seqfetch.html">Sequence
Fetcher</a>
</em></li>
<li><strong>Load Features / Annotations<br>
</strong><em>Load files describing precalculated <a
- href="../features/featuresFormat.html"
- >sequence features</a> or <a
- href="../features/annotationsFormat.html"
- >alignment annotations</a>.
+ href="../features/featuresFormat.html">sequence
+ features</a> or <a href="../features/annotationsFormat.html">alignment
+ annotations</a>.
</em></li>
<li><strong>Close (Control W)</strong><br> <em>Close
the alignment window. Make sure you have saved your
"Deselect All" to deselect all columns.</em></li>
<li><strong>Remove Right (Control R)<br>
</strong><em>If the alignment has marked columns, the alignment will
- be trimmed to the left of the leftmost marked column. To
+ be trimmed to the right of the rightmost marked column. To
mark a column, mouse click the scale bar above the
alignment. Click again to unmark a column, or select
"Deselect All" to deselect all columns.</em></li>
</strong><em>All columns which only contain gap characters
("-", ".") will be deleted.<br> You
may set the default gap character in <a
- href="../features/preferences.html"
- >preferences</a>.
+ href="../features/preferences.html">preferences</a>.
</em></li>
<li><strong>Remove All Gaps (Control Shift E)</strong><br>
<em>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.<br> You may set the default gap character in <a
- href="../features/preferences.html"
- >preferences</a>.
+ href="../features/preferences.html">preferences</a>.
</em></li>
<li><strong>Remove Redundancy (Control D)<br>
</strong><em>Selecting this option brings up a window asking you to
with alignment analysis programs which require 'properly
aligned sequences' to be all the same length.<br> You
may set the default for <strong>Pad Gaps</strong> in the <a
- href="../features/preferences.html"
- >preferences</a>.
+ href="../features/preferences.html">preferences</a>.
</em></li>
</ul></li>
<li><strong>Select</strong>
</strong><em>Selects all the sequences and residues in the
alignment. <br> Use <CTRL> and A (<APPLE>
and A on a MacOSX) to select all.
- </em></em></li>
+ </em></li>
<li><strong>Deselect All (Escape)<br>
</strong><em>Removes the current selection box (red dashed box) from
the alignment window. All selected sequences, residues and
<strong>WARNING</strong>: This cannot be undone.
</em></li>
<li><strong><a
- href="../features/columnFilterByAnnotation.html"
- >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
- or Hide columns in the alignment according to secondary
- structure, labels and values shown in alignment annotation
- rows. </em></li>
+ href="../features/columnFilterByAnnotation.html">Select/Hide
+ Columns by Annotation</a></strong> <br /> <em>Select or Hide
+ columns in the alignment according to secondary structure,
+ labels and values shown in alignment annotation rows. </em></li>
+ <li><strong>Select Highlighted Columns</strong> <br /> <em>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. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
<li><strong>Show Sequence Features</strong><br> <em>Show
or hide sequence features on this alignment.</em></li>
<li><strong><a
- href="../features/featuresettings.html"
- >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
- the Sequence Feature Settings dialog box to control the
- colour and display of sequence features on the alignment,
- and configure and retrieve features from DAS annotation
- servers.</em></li>
+ href="../features/featuresettings.html">Sequence
+ Feature Settings...</a> </strong><br> <em>Opens the
+ Sequence Feature Settings dialog box to control the colour
+ and display of sequence features on the alignment.</em></li>
<li><strong>Sequence ID Tooltip</strong><em>
(application only) <br>This submenu's options allow the
inclusion or exclusion of non-positional sequence features
rendering. </em></li>
<li><strong>Wrap<br>
</strong><em>When ticked, the alignment display is "<a
- href="../features/wrap.html"
- >wrapped</a>" 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.
+ href="../features/wrap.html">wrapped</a>" 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.
</em><br> Additional options for display of sequence numbering
and scales are also visible in wrapped layout mode:<br>
<ul>
- <li><strong>Scale Above</strong><br>
- <em> Show the alignment column position scale.</em></li>
- <li><strong>Scale Left</strong><br>
- <em> Show the sequence position for the first aligned
- residue in each row in the left column of the alignment.</em></li>
- <li><strong>Scale Right</strong><br>
- <em> Show the sequence position for the last aligned
- residue in each row in the right-most column of the
- alignment.</em></li>
+ <li><strong>Scale Above</strong><br> <em>
+ Show the alignment column position scale.</em></li>
+ <li><strong>Scale Left</strong><br> <em> Show
+ the sequence position for the first aligned residue in
+ each row in the left column of the alignment.</em></li>
+ <li><strong>Scale Right</strong><br> <em>
+ Show the sequence position for the last aligned residue
+ in each row in the right-most column of the alignment.</em></li>
<li><strong>Show Sequence Limits<br>
</strong><em>If this box is selected the sequence name will have
the start and end position of the sequence appended to
</strong><em>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.
+ rather than the left-hand edge of the alignment window.</em>
</li>
<li><strong>Show Hidden Markers<br>
</strong><em>When this box is selected, positions in the
alignment where rows and columns are hidden will be
- marked by blue arrows. </li>
+ marked by blue arrows. </em></li>
<li><strong>Boxes</strong><em><br> If this is
selected the background of a residue will be coloured
using the selected background colour. Useful if used in
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments. </em></li>
- </ul></li>
</ul></li>
</ul>
colour will be applied to all currently defined groups.<br>
</em></li>
<li><strong><a
- href="../colourSchemes/textcolour.html"
- >Colour Text...</a> </strong><em><br> 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. </em></li>
+ href="../colourSchemes/textcolour.html">Colour
+ Text...</a> </strong><em><br> 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. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
<li><strong>By Annotation</strong><br> <em>Colours
the alignment on a per-column value from a specified
annotation. See <a
- href="../colourSchemes/annotationColouring.html"
- >Annotation Colouring</a>.
+ href="../colourSchemes/annotationColouring.html">Annotation
+ Colouring</a>.
</em><br></li>
<li><strong>By RNA Helices</strong><br> <em>Colours
the helices of an RNA alignment loaded from a Stockholm file.
viewer window.
</em><br></li>
</ul></li>
- <li><strong>Calculate Tree </strong> <br> <em>Functions
- for calculating trees on the alignment or the currently
- selected region. See <a href="../calculations/tree.html">calculating
- trees</a>.
- </em>
- <ul>
- <li><strong>Neighbour Joining Using PAM250 </strong></li>
- <li><strong>Neighbour Joining Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Neighbour Joining Using Blosum62 </strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using PAM250 </strong></li>
- <li><strong>Average Distance Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Average Distance Using % Identity</strong></li>
- </ul> <strong>Note: Since Version 2.8.1, a number of
- additional similarity measures for tree calculation are
- provided in this menu.</strong></li>
- <li><strong>Pairwise Alignments</strong><br> <em>Applies
- Smith and Waterman algorithm to selected sequences. See <a
- href="../calculations/pairwise.html"
- >pairwise alignments</a>.
+ <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
+ <a href="../calculations/calculations.html">calculations dialog</a> for
+ for calculating <a href="../calculations/tree.html">trees</a> or
+ <a href="../calculations/pca.html">principle component analysis
+ plots</a> on the alignment or the currently selected
+ region.
</em><br></li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity
- scores calculated with the alignment. See <a
- href="../calculations/pca.html"
- >Principal Component Analysis</a>.
- </em> <br></li>
- <li><strong>Extract Scores ... (optional)</strong><br> <em>This
- option is only visible if Jalview detects one or more
- white-space separated values in the description line of the
- alignment sequences.<br> 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.
- </em> <br></li>
- <li><strong>Autocalculate Consensus</strong><br> <em>For
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html">pairwise
+ alignments</a>.
+ </em><br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <em>This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.<br> 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.
+ </em> <br></li>
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This
prevents the sometimes lengthy calculations performed after
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
- <li><strong>Fetch DB References</strong><br> <em>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.
- <ul>
- <li>'Trim Retrieved Sequences' - when checked, Jalview
- will discard any additional sequence data for accessions
- associated with sequences in the alignment. <br> <strong>Note:
- Disabling this could cause out of memory errors when
- working with genomic sequence records !</strong><br> <strong>Added
- in Jalview 2.8.1</strong>
- </li>
- <li>'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources<</li>
- </ul> Other sub-menus allow you to pick a specific source to query
- - sources are listed alphabetically according to their
- nickname.
- </em><br></li>
- </ul>
+ <li><strong>Fetch DB References</strong><br> <em>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.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ Disabling this could cause out of memory errors when working
+ with genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases.</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
+ </ul>
<p>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.</p>
<ul>
- <li><strong>Alignment</strong><br />
- <em> 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 <a
- href="../webServices/JABAWS.html"
- >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
- Sequence Alignment webservice client</a> entry for more
- information.
+ <li><strong>Alignment</strong><br /> <em> 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 <a
+ href="../webServices/JABAWS.html">JABAWS</a>. See the
+ <a href="../webServices/msaclient.html">Multiple Sequence
+ Alignment webservice client</a> entry for more information.
</em></li>
<li><strong>Secondary Structure Prediction</strong>
<ul>
<li><strong>JPred Secondary Structure Prediction</strong><br>
<em>Secondary structure prediction by network
- consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
+ consensus. See the <a href="../webServices/jnet.html">Jpred</a>
client entry for more information. The behaviour of this
calculation depends on the current selection:
<ul>
<li>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.</li>
<li>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.</li>
<li>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 <strong>first</strong>
+ for a JPred prediction on the <strong>first</strong>
sequence in the set (that is, the one that appears
first in the alignment window).
</li>
<li><strong>Multi-Harmony</strong><br> <em>Performs
functional residue analysis on a protein family alignment
with sub-families defined on it. See the <a
- href="../webServices/shmr.html"
- >Multi-Harmony service</a> entry for more information.
+ href="../webServices/shmr.html">Multi-Harmony
+ service</a> entry for more information.
</em></li>
</ul></li>
</ul></li>
git://source.jalview.org / jalview.git / blobdiff